WorldWideScience

Sample records for source molecular workbench

  1. Bioclipse: an open source workbench for chemo- and bioinformatics

    Directory of Open Access Journals (Sweden)

    Wagener Johannes

    2007-02-01

    Full Text Available Abstract Background There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no sucessful attempts have been made to integrate chemo- and bioinformatics into a single framework. Results Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. Conclusion Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL, an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.

  2. Data analysis workbench

    International Nuclear Information System (INIS)

    Goetz, A.; Gerring, M.; Svensson, O.; Brockhauser, S.

    2012-01-01

    Data Analysis Workbench (DAWB) is a new software tool being developed at the ESRF. Its goal is to provide a tool for both online data analysis which can be used on the beamlines and for offline data analysis which users can use during experiments or take home. The tool includes support for data visualization and work-flows. work-flows allow algorithms which exploit parallel architectures to be designed from existing high level modules for data analysis in combination with data collection. The workbench uses Passerelle as the work-flow engine and EDNA plug-ins for data analysis. Actors talking to Tango are used for sending commands to a limited set of hardware to start existing data collection algorithms. A Tango server allows work-flows to be executed from existing applications. There are scripting interfaces to Python, Javascript and SPEC. The current state at the ESRF is the workbench is in test on a selected number of beamlines. (authors)

  3. The Spoofax language workbench

    NARCIS (Netherlands)

    Kats, L.C.L.; Visser, E.

    2010-01-01

    Spoofax is a language workbench for efficient, agile development of textual domain-specific languages with state-of-the-art IDE support. It provides a comprehensive environment that integrates syntax definition, program transformation, code generation, and declarative specification of IDE components

  4. Open source molecular modeling.

    Science.gov (United States)

    Pirhadi, Somayeh; Sunseri, Jocelyn; Koes, David Ryan

    2016-09-01

    The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. An updated online version of this catalog can be found at https://opensourcemolecularmodeling.github.io. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  5. A Flexible Electronics Laboratory with Local and Remote Workbenches in a Grid

    Directory of Open Access Journals (Sweden)

    Thomas Lagö

    2008-05-01

    Full Text Available The Signal Processing Department (ASB at Blekinge Institute of Technology (BTH has created two online lab workbenches; one for electrical experiments and one for mechanical vibration experiments, mimicking and supplementing workbenches in traditional laboratories. For several years now, the workbenches have been used concurrently with on-site ones in regular, supervised lab sessions. The students are encouraged to use them on a 24/7 basis for example, in preparation for supervised sessions. The electronic workbench can be used simultaneously by many students. The aim of a project known as VISIR (Virtual Systems in Reality founded by ASB at the end of 2006, is to disseminate the online lab workbenches using open source technologies. The goal is to create a template for a grid laboratory where the nodes are workbenches for electrical experiments, located at different universities. This paper focuses on standards, pedagogical aspects, and measurement procedure requirements.

  6. Grayscale Optical Correlator Workbench

    Science.gov (United States)

    Hanan, Jay; Zhou, Hanying; Chao, Tien-Hsin

    2006-01-01

    Grayscale Optical Correlator Workbench (GOCWB) is a computer program for use in automatic target recognition (ATR). GOCWB performs ATR with an accurate simulation of a hardware grayscale optical correlator (GOC). This simulation is performed to test filters that are created in GOCWB. Thus, GOCWB can be used as a stand-alone ATR software tool or in combination with GOC hardware for building (target training), testing, and optimization of filters. The software is divided into three main parts, denoted filter, testing, and training. The training part is used for assembling training images as input to a filter. The filter part is used for combining training images into a filter and optimizing that filter. The testing part is used for testing new filters and for general simulation of GOC output. The current version of GOCWB relies on the mathematical software tools from MATLAB binaries for performing matrix operations and fast Fourier transforms. Optimization of filters is based on an algorithm, known as OT-MACH, in which variables specified by the user are parameterized and the best filter is selected on the basis of an average result for correct identification of targets in multiple test images.

  7. TCW: transcriptome computational workbench.

    Science.gov (United States)

    Soderlund, Carol; Nelson, William; Willer, Mark; Gang, David R

    2013-01-01

    The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility. The Transcriptome Computational Workbench (TCW) provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms). The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina) or assembling long sequences (e.g. Sanger, 454, transcripts), annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results. It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the transcriptome. TCW is freely available from www.agcol.arizona.edu/software/tcw.

  8. TCW: transcriptome computational workbench.

    Directory of Open Access Journals (Sweden)

    Carol Soderlund

    Full Text Available BACKGROUND: The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility. METHODOLOGY: The Transcriptome Computational Workbench (TCW provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms. The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina or assembling long sequences (e.g. Sanger, 454, transcripts, annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results. CONCLUSION: It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the

  9. Analyst workbenches state of the art report

    CERN Document Server

    Rock-Evans, R

    1987-01-01

    Analyst Workbenches examines various aspects of analyst workbenches and the tasks and data that they should support. The major advances and state of the art in analyst workbenches are discussed. A comprehensive list of the available analyst workbenches, both the experimental and the commercial products, is provided. Comprised of three parts, this book begins by describing International Computers Ltd's approach to automating analysis and design. It then explains what business analysis really means, outlines the principal features of analyst workbenches, and considers the ways in which they can

  10. CH2 molecular beam source

    International Nuclear Information System (INIS)

    Porter, R.A.R.; Grosser, A.E.

    1980-01-01

    A molecular beam source of CH 2 is described. Coaxial beams of methylene halide and alkali metal react and the mixture is formed into a molecular beam. Passage through a mechanical velocity selector rotating at a suitably high speed purifies the beam, separating light, fast CH 2 from heavier, slower contaminating species

  11. Integration of Dakota into the NEAMS Workbench

    Energy Technology Data Exchange (ETDEWEB)

    Swiler, Laura Painton [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Lefebvre, Robert A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Langley, Brandon R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Thompson, Adam B. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-07-01

    This report summarizes a NEAMS (Nuclear Energy Advanced Modeling and Simulation) project focused on integrating Dakota into the NEAMS Workbench. The NEAMS Workbench, developed at Oak Ridge National Laboratory, is a new software framework that provides a graphical user interface, input file creation, parsing, validation, job execution, workflow management, and output processing for a variety of nuclear codes. Dakota is a tool developed at Sandia National Laboratories that provides a suite of uncertainty quantification and optimization algorithms. Providing Dakota within the NEAMS Workbench allows users of nuclear simulation codes to perform uncertainty and optimization studies on their nuclear codes from within a common, integrated environment. Details of the integration and parsing are provided, along with an example of Dakota running a sampling study on the fuels performance code, BISON, from within the NEAMS Workbench.

  12. ARC integration into the NEAMS Workbench

    Energy Technology Data Exchange (ETDEWEB)

    Stauff, N. [Argonne National Lab. (ANL), Argonne, IL (United States); Gaughan, N. [Argonne National Lab. (ANL), Argonne, IL (United States); Kim, T. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2017-01-01

    One of the objectives of the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Integration Product Line (IPL) is to facilitate the deployment of the high-fidelity codes developed within the program. The Workbench initiative was launched in FY-2017 by the IPL to facilitate the transition from conventional tools to high fidelity tools. The Workbench provides a common user interface for model creation, real-time validation, execution, output processing, and visualization for integrated codes.

  13. AWOB: A Collaborative Workbench for Astronomers

    Science.gov (United States)

    Kim, J. W.; Lemson, G.; Bulatovic, N.; Makarenko, V.; Vogler, A.; Voges, W.; Yao, Y.; Kiefl, R.; Koychev, S.

    2015-09-01

    We present the Astronomers Workbench (AWOB1), a web-based collaboration and publication platform for a scientific project of any size, developed in collaboration between the Max-Planck institutes of Astrophysics (MPA) and Extra-terrestrial Physics (MPE) and the Max-Planck Digital Library (MPDL). AWOB facilitates the collaboration between geographically distributed astronomers working on a common project throughout its whole scientific life cycle. AWOB does so by making it very easy for scientists to set up and manage a collaborative workspace for individual projects, where data can be uploaded and shared. It supports inviting project collaborators, provides wikis, automated mailing lists, calendars and event notification and has a built in chat facility. It allows the definition and tracking of tasks within projects and supports easy creation of e-publications for the dissemination of data and images and other resources that cannot be added to submitted papers. AWOB extends the project concept to larger scale consortia, within which it is possible to manage working groups and sub-projects. The existing AWOB instance has so far been limited to Max-Planck members and their collaborators, but will be opened to the whole astronomical community. AWOB is an open-source project and its source code is available upon request. We intend to extend AWOB's functionality also to other disciplines, and would greatly appreciate contributions from the community.

  14. The DCR Workbench: Declarative Choreographies for Collaborative Processes

    DEFF Research Database (Denmark)

    Debois, Søren; Hildebrandt, Thomas

    2017-01-01

    analysis, time analysis, enforcement, declarative subprocesses, data dependencies, translation to other declarative models, and more. This chapter introduces the Workbench and, through the features of the Workbench, surveys the DCR formalism. The Workbench is available on-line at http: //dcr.tools....

  15. Using bio.tools to generate and annotate workbench tool descriptions

    DEFF Research Database (Denmark)

    Hillion, Kenzo-Hugo; Kuzmin, Ivan; Khodak, Anton

    2017-01-01

    - which have been registered in the ELIXIR tools registry (https://bio.tools) - into workbench environments by generating tool description templates. ToolDog includes two modules. The first module analyses the source code of the bioinformatics software with language-specific plugins, and generates...

  16. Enabling systematic, harmonised and large-scale biofilms data computation: the Biofilms Experiment Workbench.

    Science.gov (United States)

    Pérez-Rodríguez, Gael; Glez-Peña, Daniel; Azevedo, Nuno F; Pereira, Maria Olívia; Fdez-Riverola, Florentino; Lourenço, Anália

    2015-03-01

    Biofilms are receiving increasing attention from the biomedical community. Biofilm-like growth within human body is considered one of the key microbial strategies to augment resistance and persistence during infectious processes. The Biofilms Experiment Workbench is a novel software workbench for the operation and analysis of biofilms experimental data. The goal is to promote the interchange and comparison of data among laboratories, providing systematic, harmonised and large-scale data computation. The workbench was developed with AIBench, an open-source Java desktop application framework for scientific software development in the domain of translational biomedicine. Implementation favours free and open-source third-parties, such as the R statistical package, and reaches for the Web services of the BiofOmics database to enable public experiment deposition. First, we summarise the novel, free, open, XML-based interchange format for encoding biofilms experimental data. Then, we describe the execution of common scenarios of operation with the new workbench, such as the creation of new experiments, the importation of data from Excel spreadsheets, the computation of analytical results, the on-demand and highly customised construction of Web publishable reports, and the comparison of results between laboratories. A considerable and varied amount of biofilms data is being generated, and there is a critical need to develop bioinformatics tools that expedite the interchange and comparison of microbiological and clinical results among laboratories. We propose a simple, open-source software infrastructure which is effective, extensible and easy to understand. The workbench is freely available for non-commercial use at http://sing.ei.uvigo.es/bew under LGPL license. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  17. Advanced circuit simulation using Multisim workbench

    CERN Document Server

    Báez-López, David; Cervantes-Villagómez, Ofelia Delfina

    2012-01-01

    Multisim is now the de facto standard for circuit simulation. It is a SPICE-based circuit simulator which combines analog, discrete-time, and mixed-mode circuits. In addition, it is the only simulator which incorporates microcontroller simulation in the same environment. It also includes a tool for printed circuit board design.Advanced Circuit Simulation Using Multisim Workbench is a companion book to Circuit Analysis Using Multisim, published by Morgan & Claypool in 2011. This new book covers advanced analyses and the creation of models and subcircuits. It also includes coverage of transmissi

  18. ANUSpect-workbench for nuclear spectroscopy

    International Nuclear Information System (INIS)

    Padmini, S.; Diwakar, M.P.; Mukhopadhyay, P.K.; Pande, S.S.; Kataria, S.K.

    2001-01-01

    Multi-channel analyzers (MCA) are used extensively in nuclear instrumentation for research in physics, radiochemistry and many other branches of science. Though large variety of MCA hardware cards and analysis software packages are available, due to incompatibilities, user cannot mix and match these as per his requirement. Here, we present the components based approach used in the design of ANUSpect workbench, so as to give the user liberty in selecting the acquisition hardware and the analysis software for gamma, X ray and alpha spectrum analysis. AnuSpect will work under different MS Windows platforms. The paper also highlights the main functional features and the present implementation status. (author)

  19. Finite element simulations with ANSYS workbench 16

    CERN Document Server

    Lee , Huei-Huang

    2015-01-01

    Finite Element Simulations with ANSYS Workbench 16 is a comprehensive and easy to understand workbook. It utilizes step-by-step instructions to help guide readers to learn finite element simulations. Twenty seven real world case studies are used throughout the book. Many of these cases are industrial or research projects the reader builds from scratch. All the files readers may need if they have trouble are available for download on the publishers website. Companion videos that demonstrate exactly how to preform each tutorial are available to readers by redeeming the access code that comes in the book. Relevant background knowledge is reviewed whenever necessary. To be efficient, the review is conceptual rather than mathematical. Key concepts are inserted whenever appropriate and summarized at the end of each chapter. Additional exercises or extension research problems are provided as homework at the end of each chapter. A learning approach emphasizing hands-on experiences spreads through this entire book. A...

  20. ANSYS workbench tutorial release 14 structural & thermal analysis using the ANSYS workbench release 14 environment

    CERN Document Server

    Lawrence, Kent L

    2012-01-01

    The exercises in ANSYS Workbench Tutorial Release 14 introduce you to effective engineering problem solving through the use of this powerful modeling, simulation and optimization software suite. Topics that are covered include solid modeling, stress analysis, conduction/convection heat transfer, thermal stress, vibration, elastic buckling and geometric/material nonlinearities. It is designed for practicing and student engineers alike and is suitable for use with an organized course of instruction or for self-study. The compact presentation includes just over 100 end-of-chapter problems covering all aspects of the tutorials.

  1. Molecular environmental science and synchrotron radiation sources

    Energy Technology Data Exchange (ETDEWEB)

    Brown, G.E. Jr. [Stanford Univ., CA (United States)

    1995-12-31

    Molecular environmental science is a relatively new field but focuses on the chemical and physical forms of toxic and/or radioactive contaminants in soils, sediments, man-made waste forms, natural waters, and the atmosphere; their possible reactions with inorganic and organic compounds, plants, and organisms in the environment; and the molecular-level factors that control their toxicity, bioavailability, and transport. The chemical speciation of a contaminant is a major factor in determining its behavior in the environment, and synchrotron-based X-ray absorption fine structure (XAFS) spectroscopy is one of the spectroscopies of choice to quantitatively determine speciation of heavy metal contaminants in situ without selective extraction or other sample treatment. The use of high-flux insertion device beam lines at synchrotron sources and multi-element array detectors has permitted XAFS studies of metals such as Se and As in natural soils at concentration levels as low as 50 ppm. The X-ray absorption near edge structure of these metals is particularly useful in determining their oxidation state. Examples of such studies will be presented, and new insertion device beam lines under development at SSRL and the Advanced Photon Source for molecular environmental science applications will be discussed.

  2. A workbench for tera-flop supercomputing

    International Nuclear Information System (INIS)

    Resch, M.M.; Kuester, U.; Mueller, M.S.; Lang, U.

    2003-01-01

    Supercomputers currently reach a peak performance in the range of TFlop/s. With but one exception - the Japanese Earth Simulator - none of these systems has so far been able to also show a level of sustained performance for a variety of applications that comes close to the peak performance. Sustained TFlop/s are therefore rarely seen. The reasons are manifold and are well known: Bandwidth and latency both for main memory and for the internal network are the key internal technical problems. Cache hierarchies with large caches can bring relief but are no remedy to the problem. However, there are not only technical problems that inhibit the full exploitation by scientists of the potential of modern supercomputers. More and more organizational issues come to the forefront. This paper shows the approach of the High Performance Computing Center Stuttgart (HLRS) to deliver a sustained performance of TFlop/s for a wide range of applications from a large group of users spread over Germany. The core of the concept is the role of the data. Around this we design a simulation workbench that hides the complexity of interacting computers, networks and file systems from the user. (authors)

  3. Language workbench user interfaces for data analysis

    Science.gov (United States)

    Benson, Victoria M.

    2015-01-01

    Biological data analysis is frequently performed with command line software. While this practice provides considerable flexibility for computationally savy individuals, such as investigators trained in bioinformatics, this also creates a barrier to the widespread use of data analysis software by investigators trained as biologists and/or clinicians. Workflow systems such as Galaxy and Taverna have been developed to try and provide generic user interfaces that can wrap command line analysis software. These solutions are useful for problems that can be solved with workflows, and that do not require specialized user interfaces. However, some types of analyses can benefit from custom user interfaces. For instance, developing biomarker models from high-throughput data is a type of analysis that can be expressed more succinctly with specialized user interfaces. Here, we show how Language Workbench (LW) technology can be used to model the biomarker development and validation process. We developed a language that models the concepts of Dataset, Endpoint, Feature Selection Method and Classifier. These high-level language concepts map directly to abstractions that analysts who develop biomarker models are familiar with. We found that user interfaces developed in the Meta-Programming System (MPS) LW provide convenient means to configure a biomarker development project, to train models and view the validation statistics. We discuss several advantages of developing user interfaces for data analysis with a LW, including increased interface consistency, portability and extension by language composition. The language developed during this experiment is distributed as an MPS plugin (available at http://campagnelab.org/software/bdval-for-mps/). PMID:25755929

  4. Language workbench user interfaces for data analysis

    Directory of Open Access Journals (Sweden)

    Victoria M. Benson

    2015-02-01

    Full Text Available Biological data analysis is frequently performed with command line software. While this practice provides considerable flexibility for computationally savy individuals, such as investigators trained in bioinformatics, this also creates a barrier to the widespread use of data analysis software by investigators trained as biologists and/or clinicians. Workflow systems such as Galaxy and Taverna have been developed to try and provide generic user interfaces that can wrap command line analysis software. These solutions are useful for problems that can be solved with workflows, and that do not require specialized user interfaces. However, some types of analyses can benefit from custom user interfaces. For instance, developing biomarker models from high-throughput data is a type of analysis that can be expressed more succinctly with specialized user interfaces. Here, we show how Language Workbench (LW technology can be used to model the biomarker development and validation process. We developed a language that models the concepts of Dataset, Endpoint, Feature Selection Method and Classifier. These high-level language concepts map directly to abstractions that analysts who develop biomarker models are familiar with. We found that user interfaces developed in the Meta-Programming System (MPS LW provide convenient means to configure a biomarker development project, to train models and view the validation statistics. We discuss several advantages of developing user interfaces for data analysis with a LW, including increased interface consistency, portability and extension by language composition. The language developed during this experiment is distributed as an MPS plugin (available at http://campagnelab.org/software/bdval-for-mps/.

  5. Finite element modeling and simulation with ANSYS workbench

    CERN Document Server

    Chen, Xiaolin

    2014-01-01

    IntroductionSome Basic ConceptsAn Example in FEA: Spring SystemOverview of ANSYS WorkbenchSummaryProblemsBars and TrussesIntroductionReview of the 1-D Elasticity TheoryModeling of TrussesFormulation of the Bar ElementExamples with Bar ElementsCase Study with ANSYS WorkbenchSummaryProblemsBeams and FramesIntroductionReview of the Beam TheoryModeling of Beams and FramesFormulation of the Beam ElementExamples with Beam ElementsCase Study with ANSYS WorkbenchSummaryProblemsTwo-Dimensional ElasticityIntroductionReview of 2-D Elasticity TheoryModeling of 2-D Elasticity ProblemsFormulation of the Pla

  6. Scalable web services for the PSIPRED Protein Analysis Workbench.

    Science.gov (United States)

    Buchan, Daniel W A; Minneci, Federico; Nugent, Tim C O; Bryson, Kevin; Jones, David T

    2013-07-01

    Here, we present the new UCL Bioinformatics Group's PSIPRED Protein Analysis Workbench. The Workbench unites all of our previously available analysis methods into a single web-based framework. The new web portal provides a greatly streamlined user interface with a number of new features to allow users to better explore their results. We offer a number of additional services to enable computationally scalable execution of our prediction methods; these include SOAP and XML-RPC web server access and new HADOOP packages. All software and services are available via the UCL Bioinformatics Group website at http://bioinf.cs.ucl.ac.uk/.

  7. Low-cost workbench client / server cores for remote experiments in electronics

    OpenAIRE

    José M. M. Ferreira; Americo Dias; Paulo Sousa; Zorica Nedic; Jan Machotka; Ozdemir Gol; Andrew Nafalski

    2010-01-01

    This paper offers an open-source solution to implement low-cost workbenches serving a wide range of remote experiments in electronics. The proposed solution comprises 1) a small (9,65 x 6,1 cm) Linux server board; 2) a server core supporting two TCP/IP communication channels, and general purpose I/O pin drivers to interface the remote experiment hardware; and 3) a client core based on a multi-tab user interface supporting text file management to exchange experiment scripts / status informatio...

  8. The portability of the "Electronics Workbench" simulation software to China

    NARCIS (Netherlands)

    Collis, Betty; Zhi-Cheng, Dong

    1993-01-01

    This article discusses the portability of the Canadian-made simulation software package, "Electronic Workbench" package (EWB) to China. As part of a larger project investigating the portability of various educational software packages, the EWB package was used in electronics instruction in China and

  9. Assessment of the Usability of the Workbench Faraday Cage Method

    OpenAIRE

    Sørensen, Morten; Franek, Ondrej; Christensen, Søren K.; Pedersen, Gert Frølund; Ebert, Hans

    2011-01-01

    The workbench Faraday Cage method (WBFC) is a time efficient module pre-compliance test regarding radiated emission. This work investigates the method’s usability and credibility and concludes that for this particular case the WBFC perform a tolerable compliance test for frequencies below 360 MHz while it is essentially useless for higher frequencies.

  10. Assessment of the Usability of the Workbench Faraday Cage Method

    DEFF Research Database (Denmark)

    Sørensen, Morten; Franek, Ondrej; Christensen, Søren K.

    2011-01-01

    The workbench Faraday Cage method (WBFC) is a time efficient module pre-compliance test regarding radiated emission. This work investigates the method’s usability and credibility and concludes that for this particular case the WBFC perform a tolerable compliance test for frequencies below 360 MHz...

  11. A source of translationally cold molecular beams

    Science.gov (United States)

    Sarkozy, Laszlo C.

    Currently the fields studying or using molecules with low kinetic energies are experiencing an unprecedented growth. Astronomers and chemists are interested in chemical reactions taking place at temperatures below or around 20 K, spectroscopists could make very precise measurements on slow molecules and molecular physicists could chart the potential energy surfaces more accurately. And the list continues. All of these experiments need slow molecules, with kinetic energies from around 10 cm-1 down to 0. Several designs of cold sources have already been made. The most interesting ones are presented. This work describes the design and the testing of a cold source based on the collisional cooling technique: the molecules of interest are cooled well below their freezing point by a precooled buffer gas. This way condensation is avoided. The source is a copper cell cooled to 4.2 K by an external liquid helium bath. The cell is filled with cold buffer gas (helium). The molecules of choice (ammonia) are injected through a narrow tube in the middle of the cell. The cold molecules leave the cell through a 1 millimeter hole. Two versions of pulsing techniques have been employed: a shutter blade which covers the source hole and opens it only for short moments, and a chopper that modulates the beam further downstream. Both produced pulse lengths around 1 millisecond. The source is tested in an experiment in which the emerging molecules are focused and detected. Time of flight technique is used to measure the kinetic energies. Two detectors have been employed: a microwave cavity to analyze the state of the molecules in the beam, and a mass spectrometer to measure the number density of the particles. The molecules coming out of the source hole are formed into a beam by an electrostatic quadrupole state selector. The quantum mechanical aspects and the elements of electrodynamics involved in the focusing are described. A computer simulation program is presented, which helped

  12. Launching an EarthCube Interoperability Workbench for Constructing Workflows and Employing Service Interfaces

    Science.gov (United States)

    Fulker, D. W.; Pearlman, F.; Pearlman, J.; Arctur, D. K.; Signell, R. P.

    2016-12-01

    A major challenge for geoscientists—and a key motivation for the National Science Foundation's EarchCube initiative—is to integrate data across disciplines, as is necessary for complex Earth-system studies such as climate change. The attendant technical and social complexities have led EarthCube participants to devise a system-of-systems architectural concept. Its centerpiece is a (virtual) interoperability workbench, around which a learning community can coalesce, supported in their evolving quests to join data from diverse sources, to synthesize new forms of data depicting Earth phenomena, and to overcome immense obstacles that arise, for example, from mismatched nomenclatures, projections, mesh geometries and spatial-temporal scales. The full architectural concept will require significant time and resources to implement, but this presentation describes a (minimal) starter kit. With a keep-it-simple mantra this workbench starter kit can fulfill the following four objectives: 1) demonstrate the feasibility of an interoperability workbench by mid-2017; 2) showcase scientifically useful examples of cross-domain interoperability, drawn, e.g., from funded EarthCube projects; 3) highlight selected aspects of EarthCube's architectural concept, such as a system of systems (SoS) linked via service interfaces; 4) demonstrate how workflows can be designed and used in a manner that enables sharing, promotes collaboration and fosters learning. The outcome, despite its simplicity, will embody service interfaces sufficient to construct—from extant components—data-integration and data-synthesis workflows involving multiple geoscience domains. Tentatively, the starter kit will build on the Jupyter Notebook web application, augmented with libraries for interfacing current services (at data centers involved in EarthCube's Council of Data Facilities, e.g.) and services developed specifically for EarthCube and spanning most geoscience domains.

  13. A hyperspectral image data exploration workbench for environmental science applications

    International Nuclear Information System (INIS)

    Woyna, M.A.; Christiansen, J.H.; Zawada, D.G.; Simunich, K.L.

    1994-01-01

    The Hyperspectral Image Data Exploration Workbench (HIDEW) software system has been developed by Argonne National Laboratory to enable analysts at Unix workstations to conveniently access and manipulate high-resolution imagery data for analysis, mapping purposes, and input to environmental modeling applications. HIDEW is fully object-oriented, including the underlying database. This system was developed as an aid to site characterization work and atmospheric research projects

  14. A hyperspectral image data exploration workbench for environmental science applications

    Energy Technology Data Exchange (ETDEWEB)

    Woyna, M.A.; Christiansen, J.H.; Zawada, D.G.; Simunich, K.L.

    1994-08-01

    The Hyperspectral Image Data Exploration Workbench (HIDEW) software system has been developed by Argonne National Laboratory to enable analysts at Unix workstations to conveniently access and manipulate high-resolution imagery data for analysis, mapping purposes, and input to environmental modeling applications. HIDEW is fully object-oriented, including the underlying database. This system was developed as an aid to site characterization work and atmospheric research projects.

  15. Using bio.tools to generate and annotate workbench tool descriptions [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Kenzo-Hugo Hillion

    2017-11-01

    Full Text Available Workbench and workflow systems such as Galaxy, Taverna, Chipster, or Common Workflow Language (CWL-based frameworks, facilitate the access to bioinformatics tools in a user-friendly, scalable and reproducible way. Still, the integration of tools in such environments remains a cumbersome, time consuming and error-prone process. A major consequence is the incomplete or outdated description of tools that are often missing important information, including parameters and metadata such as publication or links to documentation. ToolDog (Tool DescriptiOn Generator facilitates the integration of tools - which have been registered in the ELIXIR tools registry (https://bio.tools - into workbench environments by generating tool description templates. ToolDog includes two modules. The first module analyses the source code of the bioinformatics software with language-specific plugins, and generates a skeleton for a Galaxy XML or CWL tool description. The second module is dedicated to the enrichment of the generated tool description, using metadata provided by bio.tools. This last module can also be used on its own to complete or correct existing tool descriptions with missing metadata.

  16. A COMPUTATIONAL WORKBENCH ENVIRONMENT FOR VIRTUAL POWER PLANT SIMULATION

    International Nuclear Information System (INIS)

    Mike Bockelie; Dave Swensen; Martin Denison

    2002-01-01

    This is the fifth Quarterly Technical Report for DOE Cooperative Agreement No: DE-FC26-00NT41047. The goal of the project is to develop and demonstrate a computational workbench for simulating the performance of Vision 21 Power Plant Systems. Within the last quarter, our efforts have become focused on developing an improved workbench for simulating a gasifier based Vision 21 energyplex. To provide for interoperability of models developed under Vision 21 and other DOE programs, discussions have been held with DOE and other organizations developing plant simulator tools to review the possibility of establishing a common software interface or protocol to use when developing component models. A component model that employs the CCA protocol has successfully been interfaced to our CCA enabled workbench. To investigate the software protocol issue, DOE has selected a gasifier based Vision 21 energyplex configuration for use in testing and evaluating the impacts of different software interface methods. A Memo of Understanding with the Cooperative Research Centre for Coal in Sustainable Development (CCSD) in Australia has been completed that will enable collaborative research efforts on gasification issues. Preliminary results have been obtained for a CFD model of a pilot scale, entrained flow gasifier. A paper was presented at the Vision 21 Program Review Meeting at NETL (Morgantown) that summarized our accomplishments for Year One and plans for Year Two and Year Three

  17. The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs.

    Science.gov (United States)

    Stocks, Matthew B; Mohorianu, Irina; Beckers, Matthew; Paicu, Claudia; Moxon, Simon; Thody, Joshua; Dalmay, Tamas; Moulton, Vincent

    2018-05-02

    RNA interference, a highly conserved regulatory mechanism, is mediated via small RNAs. Recent technical advances enabled the analysis of larger, complex datasets and the investigation of microRNAs and the less known small interfering RNAs. However, the size and intricacy of current data requires a comprehensive set of tools, able to discriminate the patterns from the low-level, noise-like, variation; numerous and varied suggestions from the community represent an invaluable source of ideas for future tools, the ability of the community to contribute to this software is essential. We present a new version of the UEA sRNA Workbench, reconfigured to allow an easy insertion of new tools/workflows. In its released form, it comprises of a suite of tools in a user-friendly environment, with enhanced capabilities for a comprehensive processing of sRNA-seq data e.g. tools for an accurate prediction of sRNA loci (CoLIde) and miRNA loci (miRCat2), as well as workflows to guide the users through common steps such as quality checking of the input data, normalization of abundances or detection of differential expression represent the first step in sRNA-seq analyses. The UEA sRNA Workbench is available at: http://srna-workbench.cmp.uea.ac.uk The source code is available at: https://github.com/sRNAworkbenchuea/UEA_sRNA_Workbench. v.moulton@uea.ac.uk.

  18. Context-Dependent Help for the DynaLearn Modelling and Simulation Workbench

    NARCIS (Netherlands)

    Beek, W.; Bredeweg, B.; Latour, S.; Biswas, G.; Bull, S.; Kay, J.; Mitrovic, A.

    2011-01-01

    We implemented three kinds of context-dependent help for a qualitative modelling and simulation workbench called DynaLearn. We show that it is possible to generate and select assistance knowledge based on the current model, simulation results and workbench state.

  19. The UEA Small RNA Workbench: A Suite of Computational Tools for Small RNA Analysis.

    Science.gov (United States)

    Mohorianu, Irina; Stocks, Matthew Benedict; Applegate, Christopher Steven; Folkes, Leighton; Moulton, Vincent

    2017-01-01

    RNA silencing (RNA interference, RNAi) is a complex, highly conserved mechanism mediated by short, typically 20-24 nt in length, noncoding RNAs known as small RNAs (sRNAs). They act as guides for the sequence-specific transcriptional and posttranscriptional regulation of target mRNAs and play a key role in the fine-tuning of biological processes such as growth, response to stresses, or defense mechanism.High-throughput sequencing (HTS) technologies are employed to capture the expression levels of sRNA populations. The processing of the resulting big data sets facilitated the computational analysis of the sRNA patterns of variation within biological samples such as time point experiments, tissue series or various treatments. Rapid technological advances enable larger experiments, often with biological replicates leading to a vast amount of raw data. As a result, in this fast-evolving field, the existing methods for sequence characterization and prediction of interaction (regulatory) networks periodically require adapting or in extreme cases, a complete redesign to cope with the data deluge. In addition, the presence of numerous tools focused only on particular steps of HTS analysis hinders the systematic parsing of the results and their interpretation.The UEA small RNA Workbench (v1-4), described in this chapter, provides a user-friendly, modular, interactive analysis in the form of a suite of computational tools designed to process and mine sRNA datasets for interesting characteristics that can be linked back to the observed phenotypes. First, we show how to preprocess the raw sequencing output and prepare it for downstream analysis. Then we review some quality checks that can be used as a first indication of sources of variability between samples. Next we show how the Workbench can provide a comparison of the effects of different normalization approaches on the distributions of expression, enhanced methods for the identification of differentially expressed

  20. The chemistry of molecular anions in circumstellar sources

    Energy Technology Data Exchange (ETDEWEB)

    Agúndez, Marcelino [LUTH, Observatoire de Paris-Meudon, 5 Place Jules Janssen, 92190 Meudon (France); Cernicharo, José [Departamento de Astrofísica, CAB, CSIC-INTA, Ctra. de Torrejón a Ajalvir km 4, 28850 Madrid (Spain); Guélin, Michel [Institut de Radioastronomie Millimétrique, 300 rue de la Piscine, 38406 Saint Martin d' Héres (France)

    2015-01-22

    The detection of negatively charged molecules in the interstellar and circumstellar medium in the past four years has been one of the most impacting surprises in the area of molecular astrophysics. It has motivated the interest of astronomers, physicists, and chemists on the study of the spectroscopy, chemical kinetics, and prevalence of molecular anions in the different astronomical regions. Up to six different molecular anions have been discovered in space to date, the last one being the small ion CN{sup −}, which has been observed in the envelope of the carbon star IRC +10216 and which contrary to the other larger anions is not formed by electron attachment to CN, but through reactions of large carbon anions with nitrogen atoms. Here we briefly review the current status of our knowledge of the chemistry of molecular anions in space, with particular emphasis on the circumstellar source IRC +10216, which to date is the astronomical source harboring the largest variety of anions.

  1. Designers workbench: toward real-time immersive modeling

    Science.gov (United States)

    Kuester, Falko; Duchaineau, Mark A.; Hamann, Bernd; Joy, Kenneth I.; Ma, Kwan-Liu

    2000-05-01

    This paper introduces the Designers Workbench, a semi- immersive virtual environment for two-handed modeling, sculpting and analysis tasks. The paper outlines the fundamental tools, design metaphors and hardware components required for an intuitive real-time modeling system. As companies focus on streamlining productivity to cope with global competition, the migration to computer-aided design (CAD), computer-aided manufacturing, and computer-aided engineering systems has established a new backbone of modern industrial product development. However, traditionally a product design frequently originates form a clay model that, after digitization, forms the basis for the numerical description of CAD primitives. The Designers Workbench aims at closing this technology or 'digital gap' experienced by design and CAD engineers by transforming the classical design paradigm into its fully integrate digital and virtual analog allowing collaborative development in a semi- immersive virtual environment. This project emphasizes two key components form the classical product design cycle: freeform modeling and analysis. In the freedom modeling stage, content creation in the form of two-handed sculpting of arbitrary objects using polygonal, volumetric or mathematically defined primitives is emphasized, whereas the analysis component provides the tools required for pre- and post-processing steps for finite element analysis tasks applied to the created models.

  2. Collaborative WorkBench for Researchers - Work Smarter, Not Harder

    Science.gov (United States)

    Ramachandran, Rahul; Kuo, Kwo-sen; Maskey, Manil; Lynnes, Christopher

    2014-01-01

    It is important to define some commonly used terminology related to collaboration to facilitate clarity in later discussions. We define provisioning as infrastructure capabilities such as computation, storage, data, and tools provided by some agency or similarly trusted institution. Sharing is defined as the process of exchanging data, programs, and knowledge among individuals (often strangers) and groups. Collaboration is a specialized case of sharing. In collaboration, sharing with others (usually known colleagues) is done in pursuit of a common scientific goal or objective. Collaboration entails more dynamic and frequent interactions and can occur at different speeds. Synchronous collaboration occurs in real time such as editing a shared document on the fly, chatting, video conference, etc., and typically requires a peer-to-peer connection. Asynchronous collaboration is episodic in nature based on a push-pull model. Examples of asynchronous collaboration include email exchanges, blogging, repositories, etc. The purpose of a workbench is to provide a customizable framework for different applications. Since the workbench will be common to all the customized tools, it promotes building modular functionality that can be used and reused by multiple tools. The objective of our Collaborative Workbench (CWB) is thus to create such an open and extensible framework for the Earth Science community via a set of plug-ins. Our CWB is based on the Eclipse [2] Integrated Development Environment (IDE), which is designed as a small kernel containing a plug-in loader for hundreds of plug-ins. The kernel itself is an implementation of a known specification to provide an environment for the plug-ins to execute. This design enables modularity, where discrete chunks of functionality can be reused to build new applications. The minimal set of plug-ins necessary to create a client application is called the Eclipse Rich Client Platform (RCP) [3]; The Eclipse RCP also supports thousands

  3. A Versatile Internet-Accessible Electronics Workbench with Troubleshooting Capabilities

    Directory of Open Access Journals (Sweden)

    Hamidou Soumare

    2009-08-01

    Full Text Available The MIT iLab Project was established to expand the range of laboratory experiences available to students in science and engineering education. iLabs are online laboratories that enable students to conduct real experiments remotely. Recently, the iLab Project has focused on building remote laboratories around the NI-ELVIS platform, an all-in-one electronics workbench. This paper will detail our recent efforts in expanding the capabilities of ELVIS-based iLabs by enabling students to test and debug digital and analog circuits. This work will enable students to perform remote experiments characterizing digital logic elements. By merging switching capabilities with the Digital Multimeter available on the ELVIS, students will have the ability to examine and troubleshoot circuits. These added capabilities will provide educators and students with unparalleled flexibility and significantly enrich the remote laboratory experience.

  4. A hyperspectral image analysis workbench for environmental science applications

    Energy Technology Data Exchange (ETDEWEB)

    Christiansen, J.H.; Zawada, D.G.; Simunich, K.L.; Slater, J.C.

    1992-10-01

    A significant challenge to the information sciences is to provide more powerful and accessible means to exploit the enormous wealth of data available from high-resolution imaging spectrometry, or ``hyperspectral`` imagery, for analysis, for mapping purposes, and for input to environmental modeling applications. As an initial response to this challenge, Argonne`s Advanced Computer Applications Center has developed a workstation-based prototype software workbench which employs Al techniques and other advanced approaches to deduce surface characteristics and extract features from the hyperspectral images. Among its current capabilities, the prototype system can classify pixels by abstract surface type. The classification process employs neural network analysis of inputs which include pixel spectra and a variety of processed image metrics, including image ``texture spectra`` derived from fractal signatures computed for subimage tiles at each wavelength.

  5. A hyperspectral image analysis workbench for environmental science applications

    Energy Technology Data Exchange (ETDEWEB)

    Christiansen, J.H.; Zawada, D.G.; Simunich, K.L.; Slater, J.C.

    1992-01-01

    A significant challenge to the information sciences is to provide more powerful and accessible means to exploit the enormous wealth of data available from high-resolution imaging spectrometry, or hyperspectral'' imagery, for analysis, for mapping purposes, and for input to environmental modeling applications. As an initial response to this challenge, Argonne's Advanced Computer Applications Center has developed a workstation-based prototype software workbench which employs Al techniques and other advanced approaches to deduce surface characteristics and extract features from the hyperspectral images. Among its current capabilities, the prototype system can classify pixels by abstract surface type. The classification process employs neural network analysis of inputs which include pixel spectra and a variety of processed image metrics, including image texture spectra'' derived from fractal signatures computed for subimage tiles at each wavelength.

  6. Evaluating the Effects of Interactivity in a Post-Editing Workbench

    DEFF Research Database (Denmark)

    Underwood, Nancy; Mesa-Lao, Bartolomé; Martinez, Mercedes Garcia

    2014-01-01

    This paper describes the field trial and subsequent evaluation of a post-editing workbench which is currently under development in the EU-funded CasMaCat project. Based on user evaluations of the initial prototype of the workbench, this second prototype of the workbench includes a number of inter...... on productivity, quality, user satisfaction and cognitive load as reflected in the post-editors’ gaze activity. These quantitative results are combined with the qualitative results derived from user questionnaires and interviews conducted with all the participants....

  7. DyNAMiC Workbench: an integrated development environment for dynamic DNA nanotechnology.

    Science.gov (United States)

    Grun, Casey; Werfel, Justin; Zhang, David Yu; Yin, Peng

    2015-10-06

    Dynamic DNA nanotechnology provides a promising avenue for implementing sophisticated assembly processes, mechanical behaviours, sensing and computation at the nanoscale. However, design of these systems is complex and error-prone, because the need to control the kinetic pathway of a system greatly increases the number of design constraints and possible failure modes for the system. Previous tools have automated some parts of the design workflow, but an integrated solution is lacking. Here, we present software implementing a three 'tier' design process: a high-level visual programming language is used to describe systems, a molecular compiler builds a DNA implementation and nucleotide sequences are generated and optimized. Additionally, our software includes tools for analysing and 'debugging' the designs in silico, and for importing/exporting designs to other commonly used software systems. The software we present is built on many existing pieces of software, but is integrated into a single package—accessible using a Web-based interface at http://molecular-systems.net/workbench. We hope that the deep integration between tools and the flexibility of this design process will lead to better experimental results, fewer experimental design iterations and the development of more complex DNA nanosystems. © 2015 The Authors.

  8. Neural networks used to monitor an experimental test workbench

    Energy Technology Data Exchange (ETDEWEB)

    Moraes, Davi Almeida; Pereira, Iraci Martinez, E-mail: dmoraes@dk8.com.br, E-mail: martinez@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2017-07-01

    This work presents the application of neural networks in an experimental workbench. This bench was developed with the purpose of conducting real time tests and data acquisition. The method applied for this work allowed to generate faulty data in a gradual and controlled way through the binary combination of double action valves. Using the SCADA application (Supervisory Control and Data Acquisition), it became possible to acquire data for analysis in Matlab / Simulink software. This bench has two reservoirs: a reservoir that has sensors for recording pressure and temperature variables for later analysis, and another reservoir that has level sensors. Four models were used to develop the respective practical experiments. In the first model, it was possible to perform all practical tests of the plant, as well as mechanical changes like repositioning of some mechanical components, piping, sensors and electrovalves. In the second model, it was noticed that the positioning of the flow meter, located after the pump output, prevented a good measurement of the flow variable. In the third model, it was perceived that the number of failures initially adopted, made the data too confusing for the neural network analysis. In the last model, it was possible to obtain a performance of 96.6% of hits after the reconfiguration for 4 controlled faults. (author)

  9. Carbon nanotube forests: a non-stick workbench for nanomanipulation

    International Nuclear Information System (INIS)

    Gjerde, Kjetil; Kjelstrup-Hansen, Jakob; Clausen, Casper H; Teo, Kenneth B K; Milne, William I; Rubahn, Horst-Guenter; Boeggild, Peter

    2006-01-01

    The ubiquitous static friction (stiction) and adhesion forces comprise a major obstacle in the manipulation of matter at the nanoscale (Falvo et al 1999 Nature 397 236; Urbakh M et al 2004 Nature 430 525). In this work it is shown that a surface coated with vertically aligned carbon nanotubes-a nanotube forest-acts as an effective non-stick workbench for the manipulation of micro-objects and fibres/wires with one or more dimensions in the nano-range. These include organic nanofibres (Balzer and Rubahn 2001 Appl. Phys. Lett. 79 3860) and microsized latex beads, which adhere strongly even to a conventional low surface-energy material like Teflon. Although organic nanofibres are attractive as device components due to their chemical adaptability, adhesion forces nearly always rule out manipulation as a route to assembly of prototype devices based on such materials, because organic materials are soft and fragile, and tend to stick to any surface. We demonstrate here that the nanotube forest due to its roughness not only exhibits very low stiction and dynamic friction; it also acts as a springy and mechanically compliant surface, making it possible to lift up and manipulate delicate nanostructures such as organic nanofibres in ways not possible on planar, rigid surfaces

  10. Neural networks used to monitor an experimental test workbench

    International Nuclear Information System (INIS)

    Moraes, Davi Almeida; Pereira, Iraci Martinez

    2017-01-01

    This work presents the application of neural networks in an experimental workbench. This bench was developed with the purpose of conducting real time tests and data acquisition. The method applied for this work allowed to generate faulty data in a gradual and controlled way through the binary combination of double action valves. Using the SCADA application (Supervisory Control and Data Acquisition), it became possible to acquire data for analysis in Matlab / Simulink software. This bench has two reservoirs: a reservoir that has sensors for recording pressure and temperature variables for later analysis, and another reservoir that has level sensors. Four models were used to develop the respective practical experiments. In the first model, it was possible to perform all practical tests of the plant, as well as mechanical changes like repositioning of some mechanical components, piping, sensors and electrovalves. In the second model, it was noticed that the positioning of the flow meter, located after the pump output, prevented a good measurement of the flow variable. In the third model, it was perceived that the number of failures initially adopted, made the data too confusing for the neural network analysis. In the last model, it was possible to obtain a performance of 96.6% of hits after the reconfiguration for 4 controlled faults. (author)

  11. A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository.

    Science.gov (United States)

    Smelter, Andrey; Moseley, Hunter N B

    2018-01-01

    variety of compressed binary file formats. The 'mwtab' package is an easy-to-use Python package that provides FAIRer utilization of the Metabolomics Workbench Data Repository. The source code is freely available on GitHub and via the Python Package Index. Documentation includes a 'User Guide', 'Tutorial', and 'API Reference'. The GitHub repository also provides 'mwtab' package unit-tests via a continuous integration service.

  12. HCI^2 Workbench: A Development Tool for Multimodal Human-Computer Interaction Systems

    NARCIS (Netherlands)

    Shen, Jie; Wenzhe, Shi; Pantic, Maja

    In this paper, we present a novel software tool designed and implemented to simplify the development process of Multimodal Human-Computer Interaction (MHCI) systems. This tool, which is called the HCI^2 Workbench, exploits a Publish / Subscribe (P/S) architecture [13] [14] to facilitate efficient

  13. A web-based virtual laboratory workbench for electrical circuits with ...

    African Journals Online (AJOL)

    A distinguishing feature of this Virtual Laboratory Workbench is that it allows the instructor flexibility in designing laboratory exercises so as to integrate specific knowledge objectives, outcome concepts and pre-requisites with the activity instructions. Another important benefit is that it has a watch-dog monitor that keeps a log ...

  14. The Artemis workbench for system-level performance evaluation of embedded systems

    NARCIS (Netherlands)

    Pimentel, A.D.

    2008-01-01

    In this paper, we present an overview of the Artemis workbench, which provides modelling and simulation methods and tools for efficient performance evaluation and exploration of heterogeneous embedded multimedia systems. More specifically, we describe the Artemis system-level modelling methodology,

  15. Multisample matrix-assisted laser desorption source for molecular beams of neutral peptides

    International Nuclear Information System (INIS)

    Lupulescu, C.; Abd El Rahim, M.; Antoine, R.; Barbaire, M.; Broyer, M.; Dagany, X.; Maurelli, J.; Rayane, D.; Dugourd, Ph.

    2006-01-01

    We developed and tested a multisample laser desorption source for producing stable molecular beams of neutral peptides. Our apparatus is based on matrix-assisted laser desorption technique. The source consists of 96 different targets which may be scanned by a software control procedure. Examples of molecular beams of neutral peptides are presented, as well as the influence of the different source parameters on the jet

  16. Finite element simulations with ANSYS workbench 17 theory, applications, case studies

    CERN Document Server

    Lee, Huei-Huang

    2017-01-01

    Finite Element Simulations with ANSYS Workbench 17 is a comprehensive and easy to understand workbook. Printed in full color, it utilizes rich graphics and step-by-step instructions to guide you through learning how to perform finite element simulations using ANSYS Workbench. Twenty seven real world case studies are used throughout the book. Many of these case studies are industrial or research projects that you build from scratch. Prebuilt project files are available for download should you run into any problems. Companion videos, that demonstrate exactly how to perform each tutorial, are also available. Relevant background knowledge is reviewed whenever necessary. To be efficient, the review is conceptual rather than mathematical. Key concepts are inserted whenever appropriate and summarized at the end of each chapter. Additional exercises or extension research problems are provided as homework at the end of each chapter. A learning approach emphasizing hands-on experiences spreads though this entire boo...

  17. Finite element simulations with ANSYS Workbench 18 theory, applications, case studies

    CERN Document Server

    Lee,\tHuei-huang

    2018-01-01

    Finite Element Simulations with ANSYS Workbench 18 is a comprehensive and easy to understand workbook. Printed in full color, it utilizes rich graphics and step-by-step instructions to guide you through learning how to perform finite element simulations using ANSYS Workbench. Twenty seven real world case studies are used throughout the book. Many of these case studies are industrial or research projects that you build from scratch. Prebuilt project files are available for download should you run into any problems. Companion videos, that demonstrate exactly how to perform each tutorial, are also available. Relevant background knowledge is reviewed whenever necessary. To be efficient, the review is conceptual rather than mathematical. Key concepts are inserted whenever appropriate and summarized at the end of each chapter. Additional exercises or extension research problems are provided as homework at the end of each chapter. A learning approach emphasizing hands-on experiences is utilized though this entire...

  18. Allele Workbench: transcriptome pipeline and interactive graphics for allele-specific expression.

    Directory of Open Access Journals (Sweden)

    Carol A Soderlund

    Full Text Available Sequencing the transcriptome can answer various questions such as determining the transcripts expressed in a given species for a specific tissue or condition, evaluating differential expression, discovering variants, and evaluating allele-specific expression. Differential expression evaluates the expression differences between different strains, tissues, and conditions. Allele-specific expression evaluates expression differences between parental alleles. Both differential expression and allele-specific expression have been studied for heterosis (hybrid vigor, where the hybrid has improved performance over the parents for one or more traits. The Allele Workbench software was developed for a heterosis study that evaluated allele-specific expression for a mouse F1 hybrid using libraries from multiple tissues with biological replicates. This software has been made into a distributable package, which includes a pipeline, a Java interface to build the database, and a Java interface for query and display of the results. The required input is a reference genome, annotation file, and one or more RNA-Seq libraries with optional replicates. It evaluates allelic imbalance at the SNP and transcript level and flags transcripts with significant opposite directional allele-specific expression. The Java interface allows the user to view data from libraries, replicates, genes, transcripts, exons, and variants, including queries on allele imbalance for selected libraries. To determine the impact of allele-specific SNPs on protein folding, variants are annotated with their effect (e.g., missense, and the parental protein sequences may be exported for protein folding analysis. The Allele Workbench processing results in transcript files and read counts that can be used as input to the previously published Transcriptome Computational Workbench, which has a new algorithm for determining a trimmed set of gene ontology terms. The software with demo files is available

  19. M3MS-16OR0401086 – Report on NEAMS Workbench Support for MOOSE Applications

    Energy Technology Data Exchange (ETDEWEB)

    Lefebvre, Robert A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Reactor and Nuclear Systems Division; Langley, Brandon R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Reactor and Nuclear Systems Division; Thompson, Adam B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Reactor and Nuclear Systems Division

    2016-09-23

    This report summarizes the status of the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Workbench from Oak Ridge National Laboratory (ORNL) and the integration of the MOOSE framework. This report marks the completion of NEAMS milestone M3MS-16OR0401086. This report documents the developed infrastructure to support the MOOSE framework applications, the applications’ results, visualization status, the collaboration that facilitated this progress, and future considerations.

  20. Using registries to integrate bioinformatics tools and services into workbench environments

    DEFF Research Database (Denmark)

    Ménager, Hervé; Kalaš, Matúš; Rapacki, Kristoffer

    2016-01-01

    The diversity and complexity of bioinformatics resources presents significant challenges to their localisation, deployment and use, creating a need for reliable systems that address these issues. Meanwhile, users demand increasingly usable and integrated ways to access and analyse data, especially......, a software component that will ease the integration of bioinformatics resources in a workbench environment, using their description provided by the existing ELIXIR Tools and Data Services Registry....

  1. Molecular characterization of bacteriophages for microbial source tracking in Korea.

    Science.gov (United States)

    Lee, Jung Eun; Lim, Mi Young; Kim, Sei Yoon; Lee, Sunghee; Lee, Heetae; Oh, Hyun-Myung; Hur, Hor-Gil; Ko, Gwangpyo

    2009-11-01

    We investigated coliphages from various fecal sources, including humans and animals, for microbial source tracking in South Korea. Both somatic and F+-specific coliphages were isolated from 43 fecal samples from farms, wild animal habitats, and human wastewater plants. Somatic coliphages were more prevalent and abundant than F+ coliphages in all of the tested fecal samples. We further characterized 311 F+ coliphage isolates using RNase sensitivity assays, PCR and reverse transcription-PCR, and nucleic acid sequencing. Phylogenetic analyses were performed based on the partial nucleic acid sequences of 311 F+ coliphages from various sources. F+ RNA coliphages were most prevalent among geese (95%) and were least prevalent in cows (5%). Among the genogroups of F+ RNA coliphages, most F+ coliphages isolated from animal fecal sources belonged to either group I or group IV, and most from human wastewater sources were in group II or III. Some of the group I coliphages were present in both human and animal source samples. F+ RNA coliphages isolated from various sources were divided into two main clusters. All F+ RNA coliphages isolated from human wastewater were grouped with Qbeta-like phages, while phages isolated from most animal sources were grouped with MS2-like phages. UniFrac significance statistical analyses revealed significant differences between human and animal bacteriophages. In the principal coordinate analysis (PCoA), F+ RNA coliphages isolated from human waste were distinctively separate from those isolated from other animal sources. However, F+ DNA coliphages were not significantly different or separate in the PCoA. These results demonstrate that proper analysis of F+ RNA coliphages can effectively distinguish fecal sources.

  2. The FOSS GIS Workbench on the GFZ Load Sharing Facility compute cluster

    Science.gov (United States)

    Löwe, P.; Klump, J.; Thaler, J.

    2012-04-01

    Compute clusters can be used as GIS workbenches, their wealth of resources allow us to take on geocomputation tasks which exceed the limitations of smaller systems. To harness these capabilities requires a Geographic Information System (GIS), able to utilize the available cluster configuration/architecture and a sufficient degree of user friendliness to allow for wide application. In this paper we report on the first successful porting of GRASS GIS, the oldest and largest Free Open Source (FOSS) GIS project, onto a compute cluster using Platform Computing's Load Sharing Facility (LSF). In 2008, GRASS6.3 was installed on the GFZ compute cluster, which at that time comprised 32 nodes. The interaction with the GIS was limited to the command line interface, which required further development to encapsulate the GRASS GIS business layer to facilitate its use by users not familiar with GRASS GIS. During the summer of 2011, multiple versions of GRASS GIS (v 6.4, 6.5 and 7.0) were installed on the upgraded GFZ compute cluster, now consisting of 234 nodes with 480 CPUs providing 3084 cores. The GFZ compute cluster currently offers 19 different processing queues with varying hardware capabilities and priorities, allowing for fine-grained scheduling and load balancing. After successful testing of core GIS functionalities, including the graphical user interface, mechanisms were developed to deploy scripted geocomputation tasks onto dedicated processing queues. The mechanisms are based on earlier work by NETELER et al. (2008). A first application of the new GIS functionality was the generation of maps of simulated tsunamis in the Mediterranean Sea for the Tsunami Atlas of the FP-7 TRIDEC Project (www.tridec-online.eu). For this, up to 500 processing nodes were used in parallel. Further trials included the processing of geometrically complex problems, requiring significant amounts of processing time. The GIS cluster successfully completed all these tasks, with processing times

  3. Molecular Epidemiologic Source Tracking of Orally Transmitted Chagas Disease, Venezuela

    Science.gov (United States)

    Segovia, Maikell; Martínez, Clara E.; Messenger, Louisa A.; Nessi, Anaibeth; Londoño, Juan C.; Espinosa, Raul; Martínez, Cinda; Alfredo, Mijares; Bonfante-Cabarcas, Rafael; Lewis, Michael D.; de Noya, Belkisyolé A.; Miles, Michael A.; Llewellyn, Martin S.

    2013-01-01

    Oral outbreaks of Chagas disease are increasingly reported in Latin America. The transitory presence of Trypanosoma cruzi parasites within contaminated foods, and the rapid consumption of those foods, precludes precise identification of outbreak origin. We report source attribution for 2 peri-urban oral outbreaks of Chagas disease in Venezuela via high resolution microsatellite typing. PMID:23768982

  4. Pumping requirements and options for molecular beam epitaxy and gas source molecular beam epitaxy/chemical beam epitaxy

    International Nuclear Information System (INIS)

    McCollum, M.J.; Plano, M.A.; Haase, M.A.; Robbins, V.M.; Jackson, S.L.; Cheng, K.Y.; Stillman, G.E.

    1989-01-01

    This paper discusses the use of gas sources in growth by MBE as a result of current interest in growth of InP/InGaAsP/InGaAs lattice matched to InP. For gas flows greater than a few sccm, pumping speed requirements dictate the use of turbomolecular or diffusion pumps. GaAs samples with high p-type mobilities have been grown with diffusion pumped molecular beam epitaxial system. According to the authors, this demonstration of the inherent cleanliness of a properly designed diffusion pumping system indicates that a diffusion pump is an excellent inexpensive and reliable choice for growth by molecular beam epitaxy and gas source molecular beam epitaxy/chemical beam epitaxy

  5. Optimization of Uranium Molecular Deposition for Alpha-Counting Sources

    Energy Technology Data Exchange (ETDEWEB)

    Monzo, Ellen [Univ. of Minnesota, Duluth, MN (United States); Parsons-Moss, Tashi [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Genetti, Victoria [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Knight, Kimberly [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-12-12

    Method development for molecular deposition of uranium onto aluminum 1100 plates was conducted with custom plating cells at Lawrence Livermore National Laboratory. The method development focused primarily on variation of electrode type, which was expected to directly influence plated sample homogeneity. Solid disc platinum and mesh platinum anodes were compared and data revealed that solid disc platinum anodes produced more homogenous uranium oxide films. However, the activity distribution also depended on the orientation of the platinum electrode relative to the aluminum cathode, starting current, and material composition of the plating cell. Experiments demonstrated these variables were difficult to control under the conditions available. Variation of plating parameters among a series of ten deposited plates yielded variations up to 30% in deposition efficiency. Teflon particles were observed on samples plated in Teflon cells, which poses a problem for alpha activity measurements of the plates. Preliminary electropolishing and chemical polishing studies were also conducted on the aluminum 1100 cathode plates.

  6. Emulation workbench for position sensitive gaseous scintillation detectors

    International Nuclear Information System (INIS)

    Pereira, L.; Margato, L.M.S.; Morozov, A.; Solovov, V.; Fraga, F. A. F.

    2015-01-01

    Position sensitive detectors based on gaseous scintillation proportional counters with Anger-type readout are being used in several research areas such as neutron detection, search for dark matter and neutrinoless double beta decay. Design and optimization of such detectors are complex and time consuming tasks. Simulations, while being a powerful tool, strongly depend on the light transfer models and demand accurate knowledge of many parameters, which are often not available. Here we describe an alternative approach based on the experimental evaluation of a detector using an isotropic point-like light source with precisely controllable light emission properties, installed on a 3D positioning system. The results obtained with the developed setup at validation conditions, when the scattered light is strongly suppressed show good agreement with simulations

  7. Pteros: fast and easy to use open-source C++ library for molecular analysis.

    Science.gov (United States)

    Yesylevskyy, Semen O

    2012-07-15

    An open-source Pteros library for molecular modeling and analysis of molecular dynamics trajectories for C++ programming language is introduced. Pteros provides a number of routine analysis operations ranging from reading and writing trajectory files and geometry transformations to structural alignment and computation of nonbonded interaction energies. The library features asynchronous trajectory reading and parallel execution of several analysis routines, which greatly simplifies development of computationally intensive trajectory analysis algorithms. Pteros programming interface is very simple and intuitive while the source code is well documented and easily extendible. Pteros is available for free under open-source Artistic License from http://sourceforge.net/projects/pteros/. Copyright © 2012 Wiley Periodicals, Inc.

  8. Integrating Online and Active Learning in a Computer-Assisted Translation Workbench

    DEFF Research Database (Denmark)

    Alabau, Vicent; González-Rubio, Jésus; Ortíz-Martínez, Daniel

    2014-01-01

    This paper describes a pilot study with a computed-assisted translation workbench aiming at testing the integration of online and active learning features. We investigate the effect of these features on translation productivity, using interactive translation prediction (ITP) as a baseline. User...... activity data were collected from five beta testers using key-logging and eye-tracking. User feedback was also collected at the end of the experiments in the form of retrospective think-aloud protocols. We found that OL performs better than ITP, especially in terms of translation speed. In addition, AL...

  9. HDX Workbench: Software for the Analysis of H/D Exchange MS Data

    Science.gov (United States)

    Pascal, Bruce D.; Willis, Scooter; Lauer, Janelle L.; Landgraf, Rachelle R.; West, Graham M.; Marciano, David; Novick, Scott; Goswami, Devrishi; Chalmers, Michael J.; Griffin, Patrick R.

    2012-09-01

    Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is an established method for the interrogation of protein conformation and dynamics. While the data analysis challenge of HDX-MS has been addressed by a number of software packages, new computational tools are needed to keep pace with the improved methods and throughput of this technique. To address these needs, we report an integrated desktop program titled HDX Workbench, which facilitates automation, management, visualization, and statistical cross-comparison of large HDX data sets. Using the software, validated data analysis can be achieved at the rate of generation. The application is available at the project home page http://hdx.florida.scripps.edu.

  10. Building a Taxonomic Data Editor: ITIS Taxonomic Workbench 6.0

    OpenAIRE

    Mitchell,David; Bowman,Lisa; Brockmeier,Christopher

    2017-01-01

    The Integrated Taxonomic Information System (ITIS - www.itis.gov) provides a regularly updated global database that currently contains over 840,000 scientific names and their hierarchy. A new rich Internet application for adding and editing ITIS data, Taxonomic Workbench 6.0, is being developed using the AngularJS framework. AngularJS is designed to take advantage of many features that are fairly recent to the web platform, facilitates a well-structured product that is easier to maintain, and...

  11. E-HOSPITAL - A Digital Workbench for Hospital Operations and Services Planning Using Information Technology and Algebraic Languages.

    Science.gov (United States)

    Gartner, Daniel; Padman, Rema

    2017-01-01

    In this paper, we describe the development of a unified framework and a digital workbench for the strategic, tactical and operational hospital management plan driven by information technology and analytics. The workbench can be used not only by multiple stakeholders in the healthcare delivery setting, but also for pedagogical purposes on topics such as healthcare analytics, services management, and information systems. This tool combines the three classical hierarchical decision-making levels in one integrated environment. At each level, several decision problems can be chosen. Extensions of mathematical models from the literature are presented and incorporated into the digital platform. In a case study using real-world data, we demonstrate how we used the workbench to inform strategic capacity planning decisions in a multi-hospital, multi-stakeholder setting in the United Kingdom.

  12. Microjet burners for molecular-beam sources and combustion studies

    Science.gov (United States)

    Groeger, Wolfgang; Fenn, John B.

    1988-09-01

    A novel microjet burner is described in which combustion is stabilized by a hot wall. The scale is so small that the entire burner flow can be passed through a nozzle only 0.2 mm or less in diameter into an evacuated chamber to form a supersonic free jet with expansion so rapid that all collisional processes in the jet gas are frozen in a microsecond or less. This burner can be used to provide high-temperature source gas for free jet expansion to produce intense beams of internally hot molecules. A more immediate use would seem to be in the analysis of combustion products and perhaps intermediates by various kinds of spectroscopies without some of the perturbation effects encountered in probe sampling of flames and other types of combustion devices. As an example of the latter application of this new tool, we present infrared emission spectra for jet gas obtained from the combustion of oxygen-hydrocarbon mixtures both fuel-rich and fuel-lean operation. In addition, we show results obtained by mass spectrometric analysis of the combustion products.

  13. A COMPUTATIONAL WORKBENCH ENVIRONMENT FOR VIRTUAL POWER PLANT SIMULATION

    Energy Technology Data Exchange (ETDEWEB)

    Mike Bockelie; Dave Swensen; Martin Denison; Adel Sarofim; Connie Senior

    2004-12-22

    , immersive environment. The Virtual Engineering Framework (VEF), in effect a prototype framework, was developed through close collaboration with NETL supported research teams from Iowa State University Virtual Reality Applications Center (ISU-VRAC) and Carnegie Mellon University (CMU). The VEF is open source, compatible across systems ranging from inexpensive desktop PCs to large-scale, immersive facilities and provides support for heterogeneous distributed computing of plant simulations. The ability to compute plant economics through an interface that coupled the CMU IECM tool to the VEF was demonstrated, and the ability to couple the VEF to Aspen Plus, a commercial flowsheet modeling tool, was demonstrated. Models were interfaced to the framework using VES-Open. Tests were performed for interfacing CAPE-Open-compliant models to the framework. Where available, the developed models and plant simulations have been benchmarked against data from the open literature. The VEF has been installed at NETL. The VEF provides simulation capabilities not available in commercial simulation tools. It provides DOE engineers, scientists, and decision makers with a flexible and extensible simulation system that can be used to reduce the time, technical risk, and cost to develop the next generation of advanced, coal-fired power systems that will have low emissions and high efficiency. Furthermore, the VEF provides a common simulation system that NETL can use to help manage Advanced Power Systems Research projects, including both combustion- and gasification-based technologies.

  14. Molecular and negative ion production by a standard electron cyclotron resonance ion source

    Energy Technology Data Exchange (ETDEWEB)

    Racz, R. [Institute of Nuclear Research (ATOMKI), Bem ter 18/c, H-4026 Debrecen (Hungary); University of Debrecen, Egyetem ter 1, H-4010 Debrecen (Hungary); Biri, S.; Juhasz, Z.; Sulik, B. [Institute of Nuclear Research (ATOMKI), Bem ter 18/c, H-4026 Debrecen (Hungary); Palinkas, J. [University of Debrecen, Egyetem ter 1, H-4010 Debrecen (Hungary)

    2012-02-15

    Molecular and negative ion beams, usually produced in special ion sources, play an increasingly important role in fundamental and applied atomic physics. The ATOMKI-ECRIS is a standard ECR ion source, designed to provide highly charged ion (HCI) plasmas and beams. In the present work, H{sup -}, O{sup -}, OH{sup -}, O{sub 2}{sup -}, C{sup -}, C{sub 60}{sup -} negative ions and H{sub 2}{sup +}, H{sub 3}{sup +}, OH{sup +}, H{sub 2}O{sup +}, H{sub 3}O{sup +}, O{sub 2}{sup +} positive molecular ions were generated in this HCI-ECRIS. Without any major modification in the source and without any commonly applied tricks (such as usage of cesium or magnetic filter), negative ion beams of several {mu}A and positive molecular ion beams in the mA range were successfully obtained.

  15. Online molecular image repository and analysis system: A multicenter collaborative open-source infrastructure for molecular imaging research and application.

    Science.gov (United States)

    Rahman, Mahabubur; Watabe, Hiroshi

    2018-05-01

    Molecular imaging serves as an important tool for researchers and clinicians to visualize and investigate complex biochemical phenomena using specialized instruments; these instruments are either used individually or in combination with targeted imaging agents to obtain images related to specific diseases with high sensitivity, specificity, and signal-to-noise ratios. However, molecular imaging, which is a multidisciplinary research field, faces several challenges, including the integration of imaging informatics with bioinformatics and medical informatics, requirement of reliable and robust image analysis algorithms, effective quality control of imaging facilities, and those related to individualized disease mapping, data sharing, software architecture, and knowledge management. As a cost-effective and open-source approach to address these challenges related to molecular imaging, we develop a flexible, transparent, and secure infrastructure, named MIRA, which stands for Molecular Imaging Repository and Analysis, primarily using the Python programming language, and a MySQL relational database system deployed on a Linux server. MIRA is designed with a centralized image archiving infrastructure and information database so that a multicenter collaborative informatics platform can be built. The capability of dealing with metadata, image file format normalization, and storing and viewing different types of documents and multimedia files make MIRA considerably flexible. With features like logging, auditing, commenting, sharing, and searching, MIRA is useful as an Electronic Laboratory Notebook for effective knowledge management. In addition, the centralized approach for MIRA facilitates on-the-fly access to all its features remotely through any web browser. Furthermore, the open-source approach provides the opportunity for sustainable continued development. MIRA offers an infrastructure that can be used as cross-boundary collaborative MI research platform for the rapid

  16. Atomic and molecular spectroscopy with optical-frequency-comb-referenced IR coherent sources

    International Nuclear Information System (INIS)

    Cancio, P.; Bartalini, S.; De Rosa, M.; Giusfredi, G.; Mazzotti, D.; Maddaloni, P.; Vitiello, M. S.; De Natale, P.

    2013-01-01

    We provide a review of progress in the development of metrological-grade measurements in atomic and molecular systems through the extension, in the mid-infrared and far-infrared range, of optical frequency combs (OFCs) and the introduction of new techniques and highly coherent sources. (authors)

  17. WORKBENCH FOR CONTROL SYSTEMS TRIALS BASED ON VIPA 300 CONTROLLER AND ADVANTECH INPUT/OUTPUT CARD

    Directory of Open Access Journals (Sweden)

    M. V. Levinskyi

    2015-01-01

    Full Text Available The topic is about workbench creation for control systems trials based on VIPA 300 industrial PLC and model of control object which is implemented in MatLab Simulink program on PC. Connection between controller and the PC is provided by the Advantech PCI-1711 input/output card of discrete and analog signals. Object identification,control system synthesis, creation of control device structure and its parametrical identification, as a rule, is done on a PC in a modelling environment, e.g. in MatLab. But often, using this PC modelling, the hardware and software features of algorithms which were obtained during system synthesis are not considered in a specific industrial PLC.It is considered a good idea to use a composite version where obtained algorithms are tested in a real industrial PLC and control object is substituted by a model which is working on a PC in real time scale. In this case software realization of algorithms in a specific PLC are fully taken into account and substitution of real control object by itsmodel considerably reduces the costs for carrying out experiments and allows to study the system behavior when control object parameters and modes of operation vary greatly. The creation of workbench stipulates several stages: configuration and programming of industrial PLC VIPA 313 SC, installation and configuration of Advantech PCI- 1711 input/output card, tuning of Simulink modelling environment for working in real time scale using Real-Time Windows Target Library, testing of workbench by using constant and harmonic signals of different frequencies. Work results of virtual stabilization system are compared with combined version. In virtual stabilization system PID governor and control object are implemented in Simulink. In combined version control object is still implemented in Simulink and PID governor - in VIPA 313 SC controller (using functional block FB58 from Step7 standard library.

  18. A new approach to the method of source-sink potentials for molecular conduction

    Energy Technology Data Exchange (ETDEWEB)

    Pickup, Barry T., E-mail: B.T.Pickup@sheffield.ac.uk, E-mail: P.W.Fowler@sheffield.ac.uk; Fowler, Patrick W., E-mail: B.T.Pickup@sheffield.ac.uk, E-mail: P.W.Fowler@sheffield.ac.uk; Borg, Martha [Department of Chemistry, University of Sheffield, Sheffield S3 7HF (United Kingdom); Sciriha, Irene [Department of Mathematics, University of Malta, Msida (Malta)

    2015-11-21

    We re-derive the tight-binding source-sink potential (SSP) equations for ballistic conduction through conjugated molecular structures in a form that avoids singularities. This enables derivation of new results for families of molecular devices in terms of eigenvectors and eigenvalues of the adjacency matrix of the molecular graph. In particular, we define the transmission of electrons through individual molecular orbitals (MO) and through MO shells. We make explicit the behaviour of the total current and individual MO and shell currents at molecular eigenvalues. A rich variety of behaviour is found. A SSP device has specific insulation or conduction at an eigenvalue of the molecular graph (a root of the characteristic polynomial) according to the multiplicities of that value in the spectra of four defined device polynomials. Conduction near eigenvalues is dominated by the transmission curves of nearby shells. A shell may be inert or active. An inert shell does not conduct at any energy, not even at its own eigenvalue. Conduction may occur at the eigenvalue of an inert shell, but is then carried entirely by other shells. If a shell is active, it carries all conduction at its own eigenvalue. For bipartite molecular graphs (alternant molecules), orbital conduction properties are governed by a pairing theorem. Inertness of shells for families such as chains and rings is predicted by selection rules based on node counting and degeneracy.

  19. mmpdb: An Open-Source Matched Molecular Pair Platform for Large Multiproperty Data Sets.

    Science.gov (United States)

    Dalke, Andrew; Hert, Jérôme; Kramer, Christian

    2018-05-29

    Matched molecular pair analysis (MMPA) enables the automated and systematic compilation of medicinal chemistry rules from compound/property data sets. Here we present mmpdb, an open-source matched molecular pair (MMP) platform to create, compile, store, retrieve, and use MMP rules. mmpdb is suitable for the large data sets typically found in pharmaceutical and agrochemical companies and provides new algorithms for fragment canonicalization and stereochemistry handling. The platform is written in Python and based on the RDKit toolkit. It is freely available from https://github.com/rdkit/mmpdb .

  20. Identification of the sources of primary organic aerosols at urban schools: A molecular marker approach

    International Nuclear Information System (INIS)

    Crilley, Leigh R.; Qadir, Raeed M.; Ayoko, Godwin A.; Schnelle-Kreis, Jürgen; Abbaszade, Gülcin; Orasche, Jürgen; Zimmermann, Ralf; Morawska, Lidia

    2014-01-01

    Children are particularly susceptible to air pollution and schools are examples of urban microenvironments that can account for a large portion of children's exposure to airborne particles. Thus this paper aimed to determine the sources of primary airborne particles that children are exposed to at school by analyzing selected organic molecular markers at 11 urban schools in Brisbane, Australia. Positive matrix factorization analysis identified four sources at the schools: vehicle emissions, biomass burning, meat cooking and plant wax emissions accounting for 45%, 29%, 16% and 7%, of the organic carbon respectively. Biomass burning peaked in winter due to prescribed burning of bushland around Brisbane. Overall, the results indicated that both local (traffic) and regional (biomass burning) sources of primary organic aerosols influence the levels of ambient particles that children are exposed at the schools. These results have implications for potential control strategies for mitigating exposure at schools. - Highlights: • Selected organic molecular markers at 11 urban schools were analyzed. • Four sources of primary organic aerosols were identified by PMF at the schools. • Both local and regional sources were found to influence exposure at the schools. • The results have implications for mitigation of children's exposure at schools. - The identification of the most important sources of primary organic aerosols at urban schools has implications for control strategies for mitigating children's exposure at schools

  1. Bio-functions and molecular carbohydrate structure association study in forage with different source origins revealed using non-destructive vibrational molecular spectroscopy techniques.

    Science.gov (United States)

    Ji, Cuiying; Zhang, Xuewei; Yan, Xiaogang; Mostafizar Rahman, M; Prates, Luciana L; Yu, Peiqiang

    2017-08-05

    The objectives of this study were to: 1) investigate forage carbohydrate molecular structure profiles; 2) bio-functions in terms of CHO rumen degradation characteristics and hourly effective degradation ratio of N to OM (HED N/OM ), and 3) quantify interactive association between molecular structures, bio-functions and nutrient availability. The vibrational molecular spectroscopy was applied to investigate the structure feature on a molecular basis. Two sourced-origin alfalfa forages were used as modeled forages. The results showed that the carbohydrate molecular structure profiles were highly linked to the bio-functions in terms of rumen degradation characteristics and hourly effective degradation ratio. The molecular spectroscopic technique can be used to detect forage carbohydrate structure features on a molecular basis and can be used to study interactive association between forage molecular structure and bio-functions. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Near-infrared sources in the molecular cloud G35.2-0.74

    International Nuclear Information System (INIS)

    Tapia, M.; Roth, M.; Persi, P.; Ferrari-Toniolo, M.

    1985-01-01

    Near-infrared (1-4 μm) observations of the molecular cloud G35.2-0.74 reveal the presence of four infrared sources in the vicinity of two previously reported centres of recent star formation. The northern part of G35.2-0.74 contains three point sources which are interpreted as highly obscured stars. Irs 1 coincides with H 2 O and OH maser sources and seems to be a very young early-type star. The southern part of G35.2-0.74 shows a diffuse 2.2-μm source with a flux distribution in the short-wavelength region compatible with free-free emission and a large excess at lambda > or approx. 3 μm attributed to warm dust mixed with the gas. These data are consistent with a fully developed HII region. (author)

  3. Source-sink interaction: a century old concept under the light of modern molecular systems biology.

    Science.gov (United States)

    Chang, Tian-Gen; Zhu, Xin-Guang; Raines, Christine

    2017-07-20

    Many approaches to engineer source strength have been proposed to enhance crop yield potential. However, a well-co-ordinated source-sink relationship is required finally to realize the promised increase in crop yield potential in the farmer's field. Source-sink interaction has been intensively studied for decades, and a vast amount of knowledge about the interaction in different crops and under different environments has been accumulated. In this review, we first introduce the basic concepts of source, sink and their interactions, then summarize current understanding of how source and sink can be manipulated through both environmental control and genetic manipulations. We show that the source-sink interaction underlies the diverse responses of crops to the same perturbations and argue that development of a molecular systems model of source-sink interaction is required towards a rational manipulation of the source-sink relationship for increased yield. We finally discuss both bottom-up and top-down routes to develop such a model and emphasize that a community effort is needed for development of this model. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  4. The Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source

    Energy Technology Data Exchange (ETDEWEB)

    Ferguson, Ken R. [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Department of Applied Physics, Stanford University, 348 Via Pueblo, Stanford, CA 94305 (United States); Bucher, Maximilian; Bozek, John D.; Carron, Sebastian; Castagna, Jean-Charles [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Coffee, Ryan [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Pulse Institute, Stanford University and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Curiel, G. Ivan; Holmes, Michael; Krzywinski, Jacek; Messerschmidt, Marc; Minitti, Michael; Mitra, Ankush; Moeller, Stefan; Noonan, Peter; Osipov, Timur; Schorb, Sebastian; Swiggers, Michele; Wallace, Alexander; Yin, Jing [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Bostedt, Christoph, E-mail: bostedt@slac.stanford.edu [Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States); Pulse Institute, Stanford University and SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025 (United States)

    2015-04-17

    A description of the Atomic, Molecular and Optical Sciences (AMO) instrument at the Linac Coherent Light Source is presented. Recent scientific highlights illustrate the imaging, time-resolved spectroscopy and high-power density capabilities of the AMO instrument. The Atomic, Molecular and Optical Science (AMO) instrument at the Linac Coherent Light Source (LCLS) provides a tight soft X-ray focus into one of three experimental endstations. The flexible instrument design is optimized for studying a wide variety of phenomena requiring peak intensity. There is a suite of spectrometers and two photon area detectors available. An optional mirror-based split-and-delay unit can be used for X-ray pump–probe experiments. Recent scientific highlights illustrate the imaging, time-resolved spectroscopy and high-power density capabilities of the AMO instrument.

  5. The Advanced Light Source: A new tool for research in atomic and molecular physics

    International Nuclear Information System (INIS)

    Schlachter, F.; Robinson, A.

    1991-04-01

    The Advanced Light Source at the Lawrence Berkeley Laboratory will be the world's brightest synchrotron radiation source in the extreme ultraviolet and soft x-ray regions of the spectrum when it begins operation in 1993. It will be available as a national user facility to researchers in a broad range of disciplines, including materials science, atomic and molecular physics, chemistry, biology, imaging, and technology. The high brightness of the ALS will be particularly well suited to high-resolution studies of tenuous targets, such as excited atoms, ions, and clusters. 13 figs., 4 tabs

  6. Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers

    OpenAIRE

    Taïbi, Khaled; Campo, Antonio D. del; Vilagrosa Carmona, Alberto; Bellés, José M.; López-Gresa, María Pilar; Pla, Davinia; Calvete, Juan J.; López-Nicolás, José M.; Mulet, José M.

    2017-01-01

    Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine) seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of pre...

  7. Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source.

    Science.gov (United States)

    González-Candelas, Fernando; Bracho, María Alma; Wróbel, Borys; Moya, Andrés

    2013-07-19

    Molecular phylogenetic analyses are used increasingly in the epidemiological investigation of outbreaks and transmission cases involving rapidly evolving RNA viruses. Here, we present the results of such an analysis that contributed to the conviction of an anesthetist as being responsible for the infection of 275 of his patients with hepatitis C virus. We obtained sequences of the NS5B and E1-E2 regions in the viral genome for 322 patients suspected to have been infected by the doctor, and for 44 local, unrelated controls. The analysis of 4,184 cloned sequences of the E1-E2 region allowed us to exclude 47 patients from the outbreak. A subset of patients had known dates of infection. We used these data to calibrate a relaxed molecular clock and to determine a rough estimate of the time of infection for each patient. A similar analysis led to an estimate for the time of infection of the source. The date turned out to be 10 years before the detection of the outbreak. The number of patients infected was small at first, but it increased substantially in the months before the detection of the outbreak. We have developed a procedure to integrate molecular phylogenetic reconstructions of rapidly evolving viral populations into a forensic setting adequate for molecular epidemiological analysis of outbreaks and transmission events. We applied this procedure to a large outbreak of hepatitis C virus caused by a single source and the results obtained played a key role in the trial that led to the conviction of the suspected source.

  8. Integrating open-source software applications to build molecular dynamics systems.

    Science.gov (United States)

    Allen, Bruce M; Predecki, Paul K; Kumosa, Maciej

    2014-04-05

    Three open-source applications, NanoEngineer-1, packmol, and mis2lmp are integrated using an open-source file format to quickly create molecular dynamics (MD) cells for simulation. The three software applications collectively make up the open-source software (OSS) suite known as MD Studio (MDS). The software is validated through software engineering practices and is verified through simulation of the diglycidyl ether of bisphenol-a and isophorone diamine (DGEBA/IPD) system. Multiple simulations are run using the MDS software to create MD cells, and the data generated are used to calculate density, bulk modulus, and glass transition temperature of the DGEBA/IPD system. Simulation results compare well with published experimental and numerical results. The MDS software prototype confirms that OSS applications can be analyzed against real-world research requirements and integrated to create a new capability. Copyright © 2014 Wiley Periodicals, Inc.

  9. Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools.

    Science.gov (United States)

    Sud, Manish; Fahy, Eoin; Cotter, Dawn; Azam, Kenan; Vadivelu, Ilango; Burant, Charles; Edison, Arthur; Fiehn, Oliver; Higashi, Richard; Nair, K Sreekumaran; Sumner, Susan; Subramaniam, Shankar

    2016-01-04

    The Metabolomics Workbench, available at www.metabolomicsworkbench.org, is a public repository for metabolomics metadata and experimental data spanning various species and experimental platforms, metabolite standards, metabolite structures, protocols, tutorials, and training material and other educational resources. It provides a computational platform to integrate, analyze, track, deposit and disseminate large volumes of heterogeneous data from a wide variety of metabolomics studies including mass spectrometry (MS) and nuclear magnetic resonance spectrometry (NMR) data spanning over 20 different species covering all the major taxonomic categories including humans and other mammals, plants, insects, invertebrates and microorganisms. Additionally, a number of protocols are provided for a range of metabolite classes, sample types, and both MS and NMR-based studies, along with a metabolite structure database. The metabolites characterized in the studies available on the Metabolomics Workbench are linked to chemical structures in the metabolite structure database to facilitate comparative analysis across studies. The Metabolomics Workbench, part of the data coordinating effort of the National Institute of Health (NIH) Common Fund's Metabolomics Program, provides data from the Common Fund's Metabolomics Resource Cores, metabolite standards, and analysis tools to the wider metabolomics community and seeks data depositions from metabolomics researchers across the world. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Gas Source Techniques for Molecular Beam Epitaxy of Highly Mismatched Ge Alloys

    Directory of Open Access Journals (Sweden)

    Chad A. Stephenson

    2016-12-01

    Full Text Available Ge and its alloys are attractive candidates for a laser compatible with silicon integrated circuits. Dilute germanium carbide (Ge1−xCx offers a particularly interesting prospect. By using a precursor gas with a Ge4C core, C can be preferentially incorporated in substitutional sites, suppressing interstitial and C cluster defects. We present a method of reproducible and upscalable gas synthesis of tetrakis(germylmethane, or (H3Ge4C, followed by the design of a hybrid gas/solid-source molecular beam epitaxy system and subsequent growth of defect-free Ge1−xCx by molecular beam epitaxy (MBE. Secondary ion mass spectroscopy, transmission electron microscopy and contactless electroreflectance confirm the presence of carbon with very high crystal quality resulting in a decrease in the direct bandgap energy. This technique has broad applicability to growth of highly mismatched alloys by MBE.

  11. Moving Towards a Science-Driven Workbench for Earth Science Solutions

    Science.gov (United States)

    Graves, S. J.; Djorgovski, S. G.; Law, E.; Yang, C. P.; Keiser, K.

    2017-12-01

    The NSF-funded EarthCube Integration and Test Environment (ECITE) prototype was proposed as a 2015 Integrated Activities project and resulted in the prototyping of an EarthCube federated cloud environment and the Integration and Testing Framework. The ECITE team has worked with EarthCube science and technology governance committees to define the types of integration, testing and evaluation necessary to achieve and demonstrate interoperability and functionality that benefit and support the objectives of the EarthCube cyber-infrastructure. The scope of ECITE also includes reaching beyond NSF and EarthCube to work with the broader Earth science community, such as the Earth Science Information Partners (ESIP) to incorporate lessons learned from other testbed activities, and ultimately provide broader community benefits. This presentation will discuss evolving ECITE ideas for a science-driven workbench that will start with documented science use cases, map the use cases to solution scenarios that identify the available technology and data resources that match the use case, the generation of solution workflows and test plans, the testing and evaluation of the solutions in a cloud environment, and finally the documentation of identified technology and data gaps that will assist with driving the development of additional EarthCube resources.

  12. Molecular marker analysis as a guide to the sources of fine organic aerosols

    International Nuclear Information System (INIS)

    Rogge, W.F.; Cass, G.R.; Hildemann, L.M.; Simoneit, B.R.T.

    1992-07-01

    The molecular composition of fine particulate (D p ≥ 2 μm) organic aerosol emissions from the most important sources in the Los Angeles area has been determined. Likewise, ambient concentration patterns for more than 80 single organic compounds have been measured at four urban sites (West Los Angeles, Downtown Los Angeles, Pasadena, and Rubidoux) and at one remote offshore site (San Nicolas Island). It has been found that cholesterol serves as a marker compound for emissions from charbroilers and other meat cooking operations. Vehicular exhaust being emitted from diesel and gasoline powered engines can be traced in the Los Angeles atmosphere using fossil petroleum marker compounds such as steranes and pentacyclic triterpanes (e.g., hopanes). Biogenic fine particle emission sources such as plant fragments abraded from leaf surfaces by wind and weather can be traced in the urban atmosphere. Using distinct and specific source organic tracers or assemblages of organic compounds characteristic for the sources considered it is possible to estimate the influence of different source types at any urban site where atmospheric data are available

  13. Molecular line study of massive star-forming regions from the Red MSX Source survey

    Science.gov (United States)

    Yu, Naiping; Wang, Jun-Jie

    2014-05-01

    In this paper, we have selected a sample of massive star-forming regions from the Red MSX Source survey, in order to study star formation activities (mainly outflow and inflow signatures). We have focused on three molecular lines from the Millimeter Astronomy Legacy Team Survey at 90 GHz: HCO+(1-0), H13CO+(1-0) and SiO(2-1). According to previous observations, our sources can be divided into two groups: nine massive young stellar object candidates (radio-quiet) and 10 H II regions (which have spherical or unresolved radio emissions). Outflow activities have been found in 11 sources, while only three show inflow signatures in all. The high outflow detection rate means that outflows are common in massive star-forming regions. The inflow detection rate was relatively low. We suggest that this was because of the beam dilution of the telescope. All three inflow candidates have outflow(s). The outward radiation and thermal pressure from the central massive star(s) do not seem to be strong enough to halt accretion in G345.0034-00.2240. Our simple model of G318.9480-00.1969 shows that it has an infall velocity of about 1.8 km s-1. The spectral energy distribution analysis agrees our sources are massive and intermediate-massive star formation regions.

  14. Molecular Approaches to Understanding Transmission and Source Attribution in Nontyphoidal Salmonella and Their Application in Africa.

    Science.gov (United States)

    Mather, Alison E; Vaughan, Timothy G; French, Nigel P

    2015-11-01

    Nontyphoidal Salmonella (NTS) is a frequent cause of diarrhea around the world, yet in many African countries it is more commonly associated with invasive bacterial disease. Various source attribution models have been developed that utilize microbial subtyping data to assign cases of human NTS infection to different animal populations and foods of animal origin. Advances in molecular microbial subtyping approaches, in particular whole-genome sequencing, provide higher resolution data with which to investigate these sources. In this review, we provide updates on the source attribution models developed for Salmonella, and examine the application of whole-genome sequencing data combined with evolutionary modeling to investigate the putative sources and transmission pathways of NTS, with a focus on the epidemiology of NTS in Africa. This is essential information to decide where, what, and how control strategies might be applied most effectively. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  15. Sensitivity of molecular marker-based CMB models to biomass burning source profiles

    Science.gov (United States)

    Sheesley, Rebecca J.; Schauer, James J.; Zheng, Mei; Wang, Bo

    To assess the contribution of sources to fine particulate organic carbon (OC) at four sites in North Carolina, USA, a molecular marker chemical mass balance model (MM-CMB) was used to quantify seasonal contributions for 2 years. The biomass burning contribution at these sites was found to be 30-50% of the annual OC concentration. In order to provide a better understanding of the uncertainty in MM-CMB model results, a biomass burning profile sensitivity test was performed on the 18 seasonal composites. The results using reconstructed emission profiles based on published profiles compared well, while model results using a single source test profile resulted in biomass burning contributions that were more variable. The biomass burning contribution calculated using an average regional profile of fireplace emissions from five southeastern tree species also compared well with an average profile of open burning of pine-dominated forest from Georgia. The standard deviation of the results using different source profiles was a little over 30% of the annual average biomass contributions. Because the biomass burning contribution accounted for 30-50% of the OC at these sites, the choice of profile also impacted the motor vehicle source attribution due to the common emission of elemental carbon and polycyclic aromatic hydrocarbons. The total mobile organic carbon contribution was less effected by the biomass burning profile than the relative contributions from gasoline and diesel engines.

  16. Further studies of the role of dense molecular clouds around outflow sources

    International Nuclear Information System (INIS)

    Verdes-Montenegro, L.; Torrelles, J.M.; Rodriguez, L.F.; Anglada, G.; Lopez, R.

    1989-01-01

    The (J,K) = (1,1) and (2,2) ammonia inversion transitions toward six regions with active star formation and evidence of gas outflows have been observed. Ammonia emission has been detected and mapped in five of these regions: AFGL 5142, AFGL 5157, AFGL 6366S, HHL 73, and S140N. NH3 (2,2) emission was detected toward the peak of the NH3 (1,1) core of AFGL 5157 and S140N. A rotational temperature of T(R) (2,2;1,1) = about 16 K was estimated for the two regions. Two new H2O masers of intense emission, S(nu) greater or equal 40 Jy, were detected toward the ammonia cores of AFGL 5142 and AFGL 5157. It is clear that the dense NH3 gas is closely associated with the star formation activities, since the ammonia cores in all peak close to the centers of activity. In particular, the AFGL 5157 ammonia condensation coincides with the geometrical center of a bipolar molecular outflow, suggesting that the exciting source is embedded in the ammonia core. In contrast, the molecular outflow in the AFGL 6366S region is located at the southeast edge of the NH3 condensation, suggesting that the exciting source is outside the ammonia core and that the morphology of the outflow may be influenced by the interaction with the dense ambient gas. 52 refs

  17. Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers.

    Science.gov (United States)

    Taïbi, Khaled; Del Campo, Antonio D; Vilagrosa, Alberto; Bellés, José M; López-Gresa, María Pilar; Pla, Davinia; Calvete, Juan J; López-Nicolás, José M; Mulet, José M

    2017-01-01

    Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine) seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of predicting the ability of formerly uncharacterized seedlings to cope with drought stress. Gas-exchange, water potential, photosynthetic pigments, soluble sugars, free amino acids, glutathione and proteomic analyses were carried out on control and drought-stressed seedlings in greenhouse conditions. Gas-exchange determinations were also assessed in field-planted seedlings in order to validate the greenhouse experimental conditions. Drought-tolerant seed sources presented higher values of photosynthetic rates, water use efficiency, photosynthetic pigments and soluble carbohydrates concentrations. We observed the same pattern of variation of photosynthesis rate and maximal efficiency of PSII in field. Interestingly drought-tolerant seed sources exhibited increased levels of glutathione, methionine and cysteine. The proteomic profile of drought tolerant seedlings identified two heat shock proteins and an enzyme related to methionine biosynthesis that were not present in drought sensitive seedlings, pointing to the synthesis of sulfur amino acids as a limiting factor for drought tolerance in Pinus halepensis . Our results established physiological and molecular traits useful as distinctive markers to predict drought tolerance in Pinus halepensis provenances that could be reliably used in reforestation programs in drought prone areas.

  18. Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers

    Directory of Open Access Journals (Sweden)

    Khaled Taïbi

    2017-07-01

    Full Text Available Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of predicting the ability of formerly uncharacterized seedlings to cope with drought stress. Gas-exchange, water potential, photosynthetic pigments, soluble sugars, free amino acids, glutathione and proteomic analyses were carried out on control and drought-stressed seedlings in greenhouse conditions. Gas-exchange determinations were also assessed in field-planted seedlings in order to validate the greenhouse experimental conditions. Drought-tolerant seed sources presented higher values of photosynthetic rates, water use efficiency, photosynthetic pigments and soluble carbohydrates concentrations. We observed the same pattern of variation of photosynthesis rate and maximal efficiency of PSII in field. Interestingly drought-tolerant seed sources exhibited increased levels of glutathione, methionine and cysteine. The proteomic profile of drought tolerant seedlings identified two heat shock proteins and an enzyme related to methionine biosynthesis that were not present in drought sensitive seedlings, pointing to the synthesis of sulfur amino acids as a limiting factor for drought tolerance in Pinus halepensis. Our results established physiological and molecular traits useful as distinctive markers to predict drought tolerance in Pinus halepensis provenances that could be reliably used in reforestation programs in drought prone areas.

  19. An agile acquisition decision-support workbench for evaluating ISR effectiveness

    Science.gov (United States)

    Stouch, Daniel W.; Champagne, Valerie; Mow, Christopher; Rosenberg, Brad; Serrin, Joshua

    2011-06-01

    The U.S. Air Force is consistently evolving to support current and future operations through the planning and execution of intelligence, surveillance and reconnaissance (ISR) missions. However, it is a challenge to maintain a precise awareness of current and emerging ISR capabilities to properly prepare for future conflicts. We present a decisionsupport tool for acquisition managers to empirically compare ISR capabilities and approaches to employing them, thereby enabling the DoD to acquire ISR platforms and sensors that provide the greatest return on investment. We have developed an analysis environment to perform modeling and simulation-based experiments to objectively compare alternatives. First, the analyst specifies an operational scenario for an area of operations by providing terrain and threat information; a set of nominated collections; sensor and platform capabilities; and processing, exploitation, and dissemination (PED) capacities. Next, the analyst selects and configures ISR collection strategies to generate collection plans. The analyst then defines customizable measures of effectiveness or performance to compute during the experiment. Finally, the analyst empirically compares the efficacy of each solution and generates concise reports to document their conclusions, providing traceable evidence for acquisition decisions. Our capability demonstrates the utility of using a workbench environment for analysts to design and run experiments. Crafting impartial metrics enables the acquisition manager to focus on evaluating solutions based on specific military needs. Finally, the metric and collection plan visualizations provide an intuitive understanding of the suitability of particular solutions. This facilitates a more agile acquisition strategy that handles rapidly changing technology in response to current military needs.

  20. FiGS: a filter-based gene selection workbench for microarray data

    Directory of Open Access Journals (Sweden)

    Yun Taegyun

    2010-01-01

    Full Text Available Abstract Background The selection of genes that discriminate disease classes from microarray data is widely used for the identification of diagnostic biomarkers. Although various gene selection methods are currently available and some of them have shown excellent performance, no single method can retain the best performance for all types of microarray datasets. It is desirable to use a comparative approach to find the best gene selection result after rigorous test of different methodological strategies for a given microarray dataset. Results FiGS is a web-based workbench that automatically compares various gene selection procedures and provides the optimal gene selection result for an input microarray dataset. FiGS builds up diverse gene selection procedures by aligning different feature selection techniques and classifiers. In addition to the highly reputed techniques, FiGS diversifies the gene selection procedures by incorporating gene clustering options in the feature selection step and different data pre-processing options in classifier training step. All candidate gene selection procedures are evaluated by the .632+ bootstrap errors and listed with their classification accuracies and selected gene sets. FiGS runs on parallelized computing nodes that capacitate heavy computations. FiGS is freely accessible at http://gexp.kaist.ac.kr/figs. Conclusion FiGS is an web-based application that automates an extensive search for the optimized gene selection analysis for a microarray dataset in a parallel computing environment. FiGS will provide both an efficient and comprehensive means of acquiring optimal gene sets that discriminate disease states from microarray datasets.

  1. The HARNESS Workbench: Unified and Adaptive Access to Diverse HPC Platforms

    Energy Technology Data Exchange (ETDEWEB)

    Sunderam, Vaidy S.

    2012-03-20

    The primary goal of the Harness WorkBench (HWB) project is to investigate innovative software environments that will help enhance the overall productivity of applications science on diverse HPC platforms. Two complementary frameworks were designed: one, a virtualized command toolkit for application building, deployment, and execution, that provides a common view across diverse HPC systems, in particular the DOE leadership computing platforms (Cray, IBM, SGI, and clusters); and two, a unified runtime environment that consolidates access to runtime services via an adaptive framework for execution-time and post processing activities. A prototype of the first was developed based on the concept of a 'system-call virtual machine' (SCVM), to enhance portability of the HPC application deployment process across heterogeneous high-end machines. The SCVM approach to portable builds is based on the insertion of toolkit-interpretable directives into original application build scripts. Modifications resulting from these directives preserve the semantics of the original build instruction flow. The execution of the build script is controlled by our toolkit that intercepts build script commands in a manner transparent to the end-user. We have applied this approach to a scientific production code (Gamess-US) on the Cray-XT5 machine. The second facet, termed Unibus, aims to facilitate provisioning and aggregation of multifaceted resources from resource providers and end-users perspectives. To achieve that, Unibus proposes a Capability Model and mediators (resource drivers) to virtualize access to diverse resources, and soft and successive conditioning to enable automatic and user-transparent resource provisioning. A proof of concept implementation has demonstrated the viability of this approach on high end machines, grid systems and computing clouds.

  2. Validation of the thermal code of RadTherm-IR, IR-Workbench, and F-TOM

    Science.gov (United States)

    Schwenger, Frédéric; Grossmann, Peter; Malaplate, Alain

    2009-05-01

    System assessment by image simulation requires synthetic scenarios that can be viewed by the device to be simulated. In addition to physical modeling of the camera, a reliable modeling of scene elements is necessary. Software products for modeling of target data in the IR should be capable of (i) predicting surface temperatures of scene elements over a long period of time and (ii) computing sensor views of the scenario. For such applications, FGAN-FOM acquired the software products RadTherm-IR (ThermoAnalytics Inc., Calumet, USA; IR-Workbench (OKTAL-SE, Toulouse, France). Inspection of the accuracy of simulation results by validation is necessary before using these products for applications. In the first step of validation, the performance of both "thermal solvers" was determined through comparison of the computed diurnal surface temperatures of a simple object with the corresponding values from measurements. CUBI is a rather simple geometric object with well known material parameters which makes it suitable for testing and validating object models in IR. It was used in this study as a test body. Comparison of calculated and measured surface temperature values will be presented, together with the results from the FGAN-FOM thermal object code F-TOM. In the second validation step, radiances of the simulated sensor views computed by RadTherm-IR and IR-Workbench will be compared with radiances retrieved from the recorded sensor images taken by the sensor that was simulated. Strengths and weaknesses of the models RadTherm-IR, IR-Workbench and F-TOM will be discussed.

  3. Model-based evaluation of the use of polycyclic aromatic hydrocarbons molecular diagnostic ratios as a source identification tool

    International Nuclear Information System (INIS)

    Katsoyiannis, Athanasios; Breivik, Knut

    2014-01-01

    Polycyclic Aromatic Hydrocarbons (PAHs) molecular diagnostic ratios (MDRs) are unitless concentration ratios of pair-PAHs with the same molecular weight (MW); MDRs have long been used as a tool for PAHs source identification purposes. In the present paper, the efficiency of the MDR methodology is evaluated through the use of a multimedia fate model, the calculation of characteristic travel distances (CTD) and the estimation of air concentrations for individual PAHs as a function of distance from an initial point source. The results show that PAHs with the same MW are sometimes characterized by substantially different CTDs and therefore their air concentrations and hence MDRs are predicted to change as the distance from the original source increases. From the assessed pair-PAHs, the biggest CTD difference is seen for Fluoranthene (107 km) vs. Pyrene (26 km). This study provides a strong indication that MDRs are of limited use as a source identification tool. -- Highlights: • Model-based evaluation of the PAHs molecular diagnostic ratios efficiency. • Individual PAHs are characterized by different characteristic travel distances. • MDRs are proven to be a limited tool for source identification. • Use of MDRs for other environmental media is likely unfeasible. -- PAHs molecular diagnostic ratios which change greatly as a function of distance from the emitting source are improper for source identification purposes

  4. Group III nitride-arsenide long wavelength lasers grown by elemental source molecular beam epitaxy

    International Nuclear Information System (INIS)

    Coldren, C. W.; Spruytte, S. G.; Harris, J. S.; Larson, M. C.

    2000-01-01

    Elemental source molecular beam epitaxy was used to grow InGaNAs quantum well samples, edge-emitting laser diodes, and vertical-cavity laser diodes on GaAs substrates. The quantum well samples exhibited an as-grown room temperature photoluminescence peak beyond 1310 nm which both increased dramatically in intensity and blueshifted with thermal annealing. Edge emitting laser diodes had threshold current densities as low as 450 and 750 A/cm 2 for single and triple quantum well active regions, respectively, and emitted light at 1220-1250 nm. The vertical cavity laser diodes emitted light at 1200 nm and had threshold current densities of 3 kA/cm 2 and efficiencies of 0.066 W/A. (c) 2000 American Vacuum Society

  5. Design and synthesis of single-source molecular precursors to homogeneous multi-component oxide materials

    Science.gov (United States)

    Fujdala, Kyle Lee

    This dissertation describes the syntheses of single-source molecular precursors to multi-component oxide materials. These molecules possess a core metal or element with various combinations of -OSi(O tBu)3, -O2P(OtBu) 2, and -OB[OSi(OtBu)3] 2 ligands. Such molecules decompose under mild thermolytic conditions (models for oxide-supported metal species and multi-component oxides. Significantly, the first complexes to contain three or more heteroelements suitable for use in the TMP method have been synthesized. Compounds for use as single-source molecular precursors have been synthesized containing Al, B, Cr, Hf, Mo, V, W, and Zr, and their thermal transformations have been examined. Heterogeneous catalytic reactions have been examined for selected materials. Also, cothermolyses of molecular precursors and additional molecules (i.e., metal alkoxides) have been utilized to provide materials with several components for potential use as catalysts or catalyst supports. Reactions of one and two equivs of HOSi(OtBu) 3 with Cr(OtBu)4 afforded the first Cr(IV) alkoxysiloxy complexes (tBuO) 3CrOSi(OtBu)3 and ( tBuO)2Cr[OSi(OtBu) 3]2, respectively. The high-yielding, convenient synthesis of (tBuO)3CrOSi(O tBu)3 make this complex a useful single-source molecular precursor, via the TMP method, to Cr/Si/O materials. The thermal transformations of (tBuO)3CrOSi(O tBu)3 and (tBuO) 2Cr[OSi(OtBu)3]2 to chromia-silica materials occurr at low temperatures (≤180°C), to give isobutene as the major carbon-containing product. The material generated from the solid-state conversion of (tBuO) 3CrOSi(OtBu)3 (CrOS ss) has an unexpectedly high surface area of 315 m2 g-1 that is slightly reduced to 275 m2 g-1 after calcination at 500°C in O2. The xerogel obtained by the thermolysis of an n-octane solution of (tBuO)3CrOSi(O tBu)3 (CrOSixg) has a surface area of 315 m2 g-1 that is reduced to 205 m2 g-1 upon calcination at 500°C. Powder X-ray diffraction (PXRD) analysis revealed that Cr2O 3 is

  6. Hollow-anode plasma source for molecular beam epitaxy of gallium nitride

    International Nuclear Information System (INIS)

    Anders, A.; Newman, N.; Rubin, M.; Dickinson, M.; Jones, E.; Phatak, P.; Gassmann, A.

    1996-01-01

    GaN films have been grown by molecular beam epitaxy (MBE) using a hollow-anode nitrogen plasma source. The source was developed to minimize defect formation as a result of contamination and ion damage. The hollow-anode discharge is a special form of glow discharge with very small anode area. A positive anode voltage drop of 30 endash 40 V and an increased anode sheath thickness leads to ignition of a relatively dense plasma in front of the anode hole. Driven by the pressure gradient, the open-quote open-quote anode close-quote close-quote plasma forms a bright plasma jet streaming with supersonic velocity towards the substrate. Films of GaN have been grown on (0001) SiC and (0001) Al 2 O 3 at 600 endash 800 degree C. The films were investigated by photoluminescence, cathodoluminescence, x-ray diffraction, Rutherford backscattering, and particle-induced x-ray emission. The film with the highest structural quality had a rocking curve width of 5 arcmin, the lowest reported value for MBE growth to date. copyright 1996 American Institute of Physics

  7. Molecular Ionization-Desorption Analysis Source (MIDAS) for Mass Spectrometry: Thin-Layer Chromatography

    Science.gov (United States)

    Winter, Gregory T.; Wilhide, Joshua A.; LaCourse, William R.

    2016-02-01

    Molecular ionization-desorption analysis source (MIDAS), which is a desorption atmospheric pressure chemical ionization (DAPCI) type source, for mass spectrometry has been developed as a multi-functional platform for the direct sampling of surfaces. In this article, its utility for the analysis of thin-layer chromatography (TLC) plates is highlighted. Amino acids, which are difficult to visualize without staining reagents or charring, were detected and identified directly from a TLC plate. To demonstrate the full potential of MIDAS, all active ingredients from an analgesic tablet, separated on a TLC plate, were successfully detected using both positive and negative ion modes. The identity of each of the compounds was confirmed from their mass spectra and compared against standards. Post separation, the chemical signal (blue permanent marker) as reference marks placed at the origin and solvent front were used to calculate retention factor (Rf) values from the resulting ion chromatogram. The quantitative capabilities of the device were exhibited by scanning caffeine spots on a TLC plate of increasing sample amount. A linear curve based on peak are, R2 = 0.994, was generated for seven spots ranging from 50 to 1000 ng of caffeine per spot.

  8. Practical Application of Aptamer-Based Biosensors in Detection of Low Molecular Weight Pollutants in Water Sources

    Directory of Open Access Journals (Sweden)

    Wei Zhang

    2018-02-01

    Full Text Available Water pollution has become one of the leading causes of human health problems. Low molecular weight pollutants, even at trace concentrations in water sources, have aroused global attention due to their toxicity after long-time exposure. There is an increased demand for appropriate methods to detect these pollutants in aquatic systems. Aptamers, single-stranded DNA or RNA, have high affinity and specificity to each of their target molecule, similar to antigen-antibody interaction. Aptamers can be selected using a method called Systematic Evolution of Ligands by EXponential enrichment (SELEX. Recent years we have witnessed great progress in developing aptamer selection and aptamer-based sensors for low molecular weight pollutants in water sources, such as tap water, seawater, lake water, river water, as well as wastewater and its effluents. This review provides an overview of aptamer-based methods as a novel approach for detecting low molecular weight pollutants in water sources.

  9. Detailed Source-Specific Molecular Composition of Ambient Aerosol Organic Matter Using Ultrahigh Resolution Mass Spectrometry and 1H NMR

    Directory of Open Access Journals (Sweden)

    Amanda S. Willoughby

    2016-06-01

    Full Text Available Organic aerosols (OA are universally regarded as an important component of the atmosphere that have far-ranging impacts on climate forcing and human health. Many of these impacts are related to OA molecular characteristics. Despite the acknowledged importance, current uncertainties related to the source apportionment of molecular properties and environmental impacts make it difficult to confidently predict the net impacts of OA. Here we evaluate the specific molecular compounds as well as bulk structural properties of total suspended particulates in ambient OA collected from key emission sources (marine, biomass burning, and urban using ultrahigh resolution mass spectrometry (UHR-MS and proton nuclear magnetic resonance spectroscopy (1H NMR. UHR-MS and 1H NMR show that OA within each source is structurally diverse, and the molecular characteristics are described in detail. Principal component analysis (PCA revealed that (1 aromatic nitrogen species are distinguishing components for these biomass burning aerosols; (2 these urban aerosols are distinguished by having formulas with high O/C ratios and lesser aromatic and condensed aromatic formulas; and (3 these marine aerosols are distinguished by lipid-like compounds of likely marine biological origin. This study provides a unique qualitative approach for enhancing the chemical characterization of OA necessary for molecular source apportionment.

  10. Determination of sulfur in food by high resolution continuum source flame molecular absorption spectrometry

    Science.gov (United States)

    Zambrzycka, Elżbieta; Godlewska-Żyłkiewicz, Beata

    2014-11-01

    In the present work, a fast, simple and sensitive analytical method for determination of sulfur in food and beverages by high resolution continuum source flame molecular absorption spectrometry was developed. The determination was performed via molecular absorption of carbon monosulfide, CS. Different CS rotational lines (257.959 nm, 258.033 nm, 258.055 nm), number of pixels and types of standard solution of sulfur, namely: sulfuric acid, sodium sulfate, ammonium sulfate, sodium sulfite, sodium sulfide, DL-cysteine, and L-cystine, were studied in terms of sensitivity, repeatability of results as well as limit of detection and limit of quantification. The best results were obtained for measurements of absorption of the CS molecule at 258.055 nm at the wavelength range covering 3 pixels and DL-cysteine in 0.2 mol L- 1 HNO3 solution as a calibration standard. Under optimized conditions the limit of detection and the limit of quantification achieved for sulfur were 10.9 mg L- 1 and 36.4 mg L- 1, respectively. The repeatability of the results expressed as relative standard deviation was typically beverage samples with added known amount of sulfur standard. The recovery of analyte from such samples was in the range of 93-105% with the repeatability in the range of 4.1-5.0%. The developed method was applied for the determination of sulfur in milk (194 ± 10 mg kg- 1), egg white (2188 ± 29 mg kg- 1), mineral water (31.0 ± 0.9 mg L- 1), white wine (260 ± 4 mg L- 1) and red wine (82 ± 2 mg L- 1), as well as in sample rich in ions, such as bitter mineral water (6900 ± 100 mg L- 1).

  11. Molecular dynamics simulation of chemical vapor deposition of amorphous carbon. Dependence on H/C ratio of source gas

    International Nuclear Information System (INIS)

    Ito, Atsushi M.; Takayama, Arimichi; Nakamura, Hiroaki; Saito, Seiki; Ohno, Noriyasu; Kajita, Shin

    2011-01-01

    By molecular dynamics simulation, the chemical vapor deposition of amorphous carbon onto graphite and diamond surfaces was studied. In particular, we investigated the effect of source H/C ratio, which is the ratio of the number of hydrogen atoms to the number of carbon atoms in a source gas, on the deposition process. In the present simulation, the following two source gas conditions were tested: one was that the source gas was injected as isolated carbon and hydrogen atoms, and the other was that the source gas was injected as hydrocarbon molecules. Under the former condition, we found that as the source H/C ratio increases, the deposition rate of carbon atoms decreases exponentially. This exponential decrease in the deposition rate with increasing source H/C ratio agrees with experimental data. However, under the latter molecular source condition, the deposition rate did not decrease exponentially because of a chemical reaction peculiar to the type of hydrocarbon in the source gas. (author)

  12. Determination of sulfur in food by high resolution continuum source flame molecular absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Zambrzycka, Elżbieta; Godlewska-Żyłkiewicz, Beata, E-mail: bgodlew@uwb.edu.pl

    2014-11-01

    In the present work, a fast, simple and sensitive analytical method for determination of sulfur in food and beverages by high resolution continuum source flame molecular absorption spectrometry was developed. The determination was performed via molecular absorption of carbon monosulfide, CS. Different CS rotational lines (257.959 nm, 258.033 nm, 258.055 nm), number of pixels and types of standard solution of sulfur, namely: sulfuric acid, sodium sulfate, ammonium sulfate, sodium sulfite, sodium sulfide, DL-cysteine, and L-cystine, were studied in terms of sensitivity, repeatability of results as well as limit of detection and limit of quantification. The best results were obtained for measurements of absorption of the CS molecule at 258.055 nm at the wavelength range covering 3 pixels and DL-cysteine in 0.2 mol L{sup −1} HNO{sub 3} solution as a calibration standard. Under optimized conditions the limit of detection and the limit of quantification achieved for sulfur were 10.9 mg L{sup −1} and 36.4 mg L{sup −1}, respectively. The repeatability of the results expressed as relative standard deviation was typically < 5%. The accuracy of the method was tested by analysis of digested biological certified reference materials (soya bean flour, corn flour and herbs) and recovery experiment for beverage samples with added known amount of sulfur standard. The recovery of analyte from such samples was in the range of 93–105% with the repeatability in the range of 4.1–5.0%. The developed method was applied for the determination of sulfur in milk (194 ± 10 mg kg{sup −1}), egg white (2188 ± 29 mg kg{sup −1}), mineral water (31.0 ± 0.9 mg L{sup −1}), white wine (260 ± 4 mg L{sup −1}) and red wine (82 ± 2 mg L{sup −1}), as well as in sample rich in ions, such as bitter mineral water (6900 ± 100 mg L{sup −1}). - Highlights: • HR-CS FMAS technique was used for sulfur measurement via molecular absorption of carbon monosulfide, CS. • Organic DL

  13. Source-specific sewage pollution detection in urban river waters using pharmaceuticals and personal care products as molecular indicators.

    Science.gov (United States)

    Kiguchi, Osamu; Sato, Go; Kobayashi, Takashi

    2016-11-01

    Source-specific elucidation of domestic sewage pollution caused by various effluent sources in an urban river water, as conducted for this study, demands knowledge of the relation between concentrations of pharmaceuticals and personal care products (PPCPs) as molecular indicators (caffeine, carbamazepine, triclosan) and water quality concentrations of total nitrogen (T-N) and total phosphorous (T-P). River water and wastewater samples from the Asahikawa River Basin in northern Japan were analyzed using derivatization-gas chromatography/mass spectrometry. Caffeine, used as an indicator of domestic sewage in the Asahikawa River Basin, was more ubiquitous than either carbamazepine or triclosan (92-100 %). Its concentration was higher than any target compound used to assess the basin: caffeine, caffeine concentrations detected in wastewater effluents and the strongly positive mutual linear correlation between caffeine and T-N or T-P (R 2  > 0.759) reflect the contribution of septic tank system effluents to the lower Asahikawa River Basin. Results of relative molecular indicators in combination with different molecular indicators (caffeine/carbamazepine and triclosan/carbamazepine) and cluster analysis better reflect the contribution of sewage than results obtained using concentrations of respective molecular indicators and cluster analysis. Relative molecular indicators used with water quality parameters (e.g., caffeine/T-N ratio) in this study provide results more clearly, relatively, and quantitatively than results obtained using molecular indicators alone. Moreover, the caffeine/T-N ratio reflects variations of caffeine flux from effluent sources. These results suggest strongly relative molecular indicators are also useful indicators, reflecting differences in spatial contributions of domestic sources for PPCPs in urban areas.

  14. Molecular biomarkers for sources of organic matter in lacustrine sediments in a subtropical lake in China.

    Science.gov (United States)

    Wang, Yan-Hua; Yang, Hao; Chen, Xia; Zhang, Ji-Xiang; Ou, Jie; Xie, Biao; Huang, Chang-Chun

    2013-05-01

    N-alkanes distributions and stable isotopic compositions (δ(13)C and δ(15)N) in the lacustrine sediments of Shijiu lake were measured to assess whether biological source information was recorded in the molecular biomarker. Results showed regular unimodal n-alkanes distribution in range of C16-C33 with strong predominance of odd-numbered n-alkanes, maximizing at C29. The δ(15)N for SON were uniformly low, ranging from -6.7‰ to 3.8‰ and C/N ratios ranged from 6.6 to 10.0, suggesting that most of organic matter was influenced by terrestrial characteristics of the watershed. The δ(13)C for C27 to C31n-alkanes and for SOC varied from -32.9‰ to -26.6‰ and -23.4‰ to -21.6‰, respectively, falling within the range of corresponding n-alkanes in leaves mainly from C3 land plants. The values of C/N, CPI, OEP, ACL and C27/C31 exhibit similar temporal changes with the primary production, showing enhanced eutrophication resulted from increased anthropogenic activities in Shijiu lake from 1852 to 2010. Copyright © 2013 Elsevier Ltd. All rights reserved.

  15. Dye shift: a neglected source of genotyping error in molecular ecology.

    Science.gov (United States)

    Sutton, Jolene T; Robertson, Bruce C; Jamieson, Ian G

    2011-05-01

    Molecular ecologists must be vigilant in detecting and accounting for genotyping error, yet potential errors stemming from dye-induced mobility shift (dye shift) may be frequently neglected and largely unknown to researchers who employ 3-primer systems with automated genotyping. When left uncorrected, dye shift can lead to mis-scoring alleles and even to falsely calling new alleles if different dyes are used to genotype the same locus in subsequent reactions. When we used four different fluorophore labels from a standard dye set to genotype the same set of loci, differences in the resulting size estimates for a single allele ranged from 2.07 bp to 3.68 bp. The strongest effects were associated with the fluorophore PET, and relative degree of dye shift was inversely related to locus size. We found little evidence in the literature that dye shift is regularly accounted for in 3-primer studies, despite knowledge of this phenomenon existing for over a decade. However, we did find some references to erroneous standard correction factors for the same set of dyes that we tested. We thus reiterate the need for strict quality control when attempting to reduce possible sources of genotyping error, and in cases where different dyes are applied to a single locus, perhaps mistakenly, we strongly discourage researchers from assuming generic correction patterns. © 2011 Blackwell Publishing Ltd.

  16. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.

    Science.gov (United States)

    Pronk, Sander; Páll, Szilárd; Schulz, Roland; Larsson, Per; Bjelkmar, Pär; Apostolov, Rossen; Shirts, Michael R; Smith, Jeremy C; Kasson, Peter M; van der Spoel, David; Hess, Berk; Lindahl, Erik

    2013-04-01

    Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. GROMACS is an open source and free software available from http://www.gromacs.org. Supplementary data are available at Bioinformatics online.

  17. abc the aspectBench compiler for aspectJ a workbench for aspect-oriented programming language and compilers research

    DEFF Research Database (Denmark)

    Allan, Chris; Avgustinov, Pavel; Christensen, Aske Simon

    2005-01-01

    Aspect-oriented programming (AOP) is gaining popularity as a new way of modularising cross-cutting concerns. The aspectbench compiler (abc) is a new workbench for AOP research which provides an extensible research framework for both new language features and new compiler optimisations. This poste...

  18. Search for near-infrared counterparts of IRAS embedded sources in the M17 SW giant molecular cloud

    International Nuclear Information System (INIS)

    Elmegreen, D.M.; Phillips, J.; Beck, K.; Thomas, H.; Howard, J.

    1988-01-01

    Wide-field near-infrared and blue band plates of the region containing the M17 giant molecular cloud complex have been blinked to locate bright near-infrared stars that may be embedded in the M17 SW giant molecular cloud. Twenty such stars coincided with the positions of IRAS point sources that appeared embedded based on color-color diagrams. Some of these stars may be the sources of the infrared luminosities. Of the 20 stars, seven were too faint to appear on the B band plate. The optical magnitudes and colors determined from the plate image diameters were measured for the other 13 coincident stars; they are most likely upper main-sequence or pre-main-sequence stars with extinctions of 7 mag. The IRAS luminosity-temperature diagram indicates that the embedded sources in M17 are more massive than those in the Orion cloud. 35 references

  19. Evaluation of climatic vibration testing on plastic waterproof enclosure for electronic equipment using ANSYS[reg] workbench

    International Nuclear Information System (INIS)

    Aw, K.C.; Huang, W.D.J.; De Silva, M.W.R.P.

    2007-01-01

    Designing and testing of waterproof enclosure for electronic equipment involves significant amount of time and resources. This paper concentrates on electronic equipment used for maritime application. Typical waterproof test perform is based on the IEC 60529 standards and is insufficient to determine its reliability. Since, these enclosures were subjected to environmental stress such as heat and vibration and there is a need to understand how these affect the waterproof performance. Simulation using ANSYS workbench software was performed to comprehend the effect of various parameters of accelerated testing performed on these waterproof enclosures. Experiments were performed to examine the correlation with simulation results. The results confirmed that accelerated testing with random vibration at cold temperature causes greatest stress and causes degradation to adhesive bonds and hence affect the waterproof performance

  20. Molecular Characterization of Yeast Strains Isolated from Different Sources by Restriction Fragment Length Polymorphism

    International Nuclear Information System (INIS)

    Ali, M. S.; Latif, Z.

    2016-01-01

    Various molecular techniques like analysis of the amplified rDNA internal transcribed spacers (ITS), intragenic spacers and total ITS region analysis by restriction fragment length polymorphism (RFLP) has been introduced for yeast identification but there are limited databases to identify yeast species on the basis of 5.8S rDNA. In this study, twenty nine yeast strains from various sources including spoiled fruits, vegetables, foodstuffs, and concentrated juices were characterized by PCR-RFLP. PCR-RFLP has been used to characterize yeasts present in different spoiled food samples after isolation of the yeasts. By using this technique, the isolated yeast strains were characterized by direct 5.8S-ITS rDNA region amplification. RFLP analysis was applied to each of the amplification products (varied from 400bp to 800bp) detected, and the corresponding yeast identifications were made according to each specific restriction patterns obtained after treatment with two endonucleases TaqI and HaeIII which yielded a specific banding pattern for each species. For further confirmation amplified products of eleven selected isolates were sequenced and blast on NCBI. Both RFLP and sequence analyses of the strains with accession nos. KF472163, KF472164, KF472165, KF472166, KF472167, KF472168, KF472169, KF472170, KF472171, KF472172, KF472173 gave significantly similar results. The isolates were found to belong five different yeast species including; Candida spp., Pichia spp., Kluyveromyces spp., Clavispora spp. and Hanseniaspora spp. This method provides a fast, easy, reliable and authentic way for determining yeast population present in different type of samples, as compared to traditional characterization technique. (author)

  1. Molecular Epidemiology of Group A Rotaviruses in Water Sources and Selected Raw Vegetables in Southern Africa

    Science.gov (United States)

    van Zyl, W. B.; Page, N. A.; Grabow, W. O. K.; Steele, A. D.; Taylor, M. B.

    2006-01-01

    Group A rotaviruses (RVs) are the most important cause of acute viral gastroenteritis in infants and young children. In this study raw and treated drinking water supplies at plants in two geographic areas, as well as selected irrigation water and corresponding raw vegetables in three regions of southern Africa, were screened for the presence of RVs using molecular techniques. Group A RVs were detected in 11.8% of partially treated and 1.7% of finally treated drinking water samples and in 14% of irrigation water samples and 1.7% of corresponding raw vegetable samples. Type-specific reverse transcriptase-PCR and sequence analysis revealed the presence of multiple types (G1, G2, G8, and G9) in irrigation water and single types (G1 or G3) in raw and treated drinking water. Group A RVs detected in all samples consisted of mixed P types (P[4], P[6], P[8], and P[9]), with P[6] predominating. The detection of types G8, G9, and P[6] reflects the emergence of these types in clinical infections. The similarity of environmental types to those in patients with clinical RV infections confirms the value of wastewater screening as a tool for assessing RVs circulating in communities, with the benefit of detecting types that cause both clinical and subclinical infections. The results provide new information on RV types in water and related environments and identify the potential risk of waterborne transmission. In addition, the presence of RVs in drinking water underlines shortcomings in quality specifications. These data provide valuable information regarding the prevalence of RVs in environmental sources, with important implications for vaccine development. PMID:16820443

  2. New impressive capabilities of SE-workbench for EO/IR real-time rendering of animated scenarios including flares

    Science.gov (United States)

    Le Goff, Alain; Cathala, Thierry; Latger, Jean

    2015-10-01

    To provide technical assessments of EO/IR flares and self-protection systems for aircraft, DGA Information superiority resorts to synthetic image generation to model the operational battlefield of an aircraft, as viewed by EO/IR threats. For this purpose, it completed the SE-Workbench suite from OKTAL-SE with functionalities to predict a realistic aircraft IR signature and is yet integrating the real-time EO/IR rendering engine of SE-Workbench called SE-FAST-IR. This engine is a set of physics-based software and libraries that allows preparing and visualizing a 3D scene for the EO/IR domain. It takes advantage of recent advances in GPU computing techniques. The recent past evolutions that have been performed concern mainly the realistic and physical rendering of reflections, the rendering of both radiative and thermal shadows, the use of procedural techniques for the managing and the rendering of very large terrains, the implementation of Image- Based Rendering for dynamic interpolation of plume static signatures and lastly for aircraft the dynamic interpolation of thermal states. The next step is the representation of the spectral, directional, spatial and temporal signature of flares by Lacroix Defense using OKTAL-SE technology. This representation is prepared from experimental data acquired during windblast tests and high speed track tests. It is based on particle system mechanisms to model the different components of a flare. The validation of a flare model will comprise a simulation of real trials and a comparison of simulation outputs to experimental results concerning the flare signature and above all the behavior of the stimulated threat.

  3. Using rapid diagnostic tests as source of malaria parasite DNA for molecular analyses in the era of declining malaria prevalence

    DEFF Research Database (Denmark)

    Ishengoma, Deus S; Lwitiho, Sudi; Madebe, Rashid A

    2011-01-01

    was conducted to examine if sufficient DNA could be successfully extracted from malaria rapid diagnostic tests (RDTs), used and collected as part of routine case management services in health facilities, and thus forming the basis for molecular analyses, surveillance and quality control (QC) testing of RDTs....... continued molecular surveillance of malaria parasites is important to early identify emerging anti-malarial drug resistance, it is becoming increasingly difficult to obtain parasite samples from ongoing studies, such as routine drug efficacy trials. To explore other sources of parasite DNA, this study...

  4. The Exploratory Modeling Workbench : An open source toolkit for exploratory modeling, scenario discovery, and (multi-objective) robust decision making

    NARCIS (Netherlands)

    Kwakkel, J.H.

    2017-01-01

    There is a growing interest in model-based decision support under deep uncertainty, reflected in a variety of approaches being put forward in the literature. A key idea shared among these is the use of models for exploratory rather than predictive purposes. Exploratory modeling aims at exploring

  5. Atmospheric-pressure solution-cathode glow discharge: A versatile ion source for atomic and molecular mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Schwartz, Andrew J. [Department of Chemistry, Indiana University, Bloomington, IN, 47405 (United States); Williams, Kelsey L. [Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242 (United States); Hieftje, Gary M. [Department of Chemistry, Indiana University, Bloomington, IN, 47405 (United States); Shelley, Jacob T., E-mail: shellj@rpi.edu [Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242 (United States); Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180 (United States)

    2017-01-15

    An atmospheric-pressure solution-cathode glow discharge (SCGD) has been evaluated as an ion source for atomic, molecular, and ambient desorption/ionization mass spectrometry. The SCGD consists of a direct-current plasma, supported in the ambient air in the absence of gas flows, and sustained upon the surface of a flowing liquid cathode. Analytes introduced in the flowing liquid, as an ambient gas, or as a solid held near the plasma are vaporized and ionized by interactions within or near the discharge. Introduction of acidic solutions containing metal salts produced bare elemental ions as well as H{sub 2}O, OH{sup −} and NO{sub 3}{sup −} adducts. Detection limits for these elemental species ranged from 0.1 to 4 ppb, working curves spanned more than 4 orders of linear dynamic range, and precision varied between 5 and 16% relative standard deviation. Small organic molecules were also efficiently ionized from solution, and both the intact molecular ion and fragments were observed in the resulting SCGD mass spectra. Fragmentation of molecular species was found to be tunable; high discharge currents led to harder ionization, while low discharge currents produced stronger molecular-ion signals. Ambient gases and solids, desorbed by the plasma from a glass probe, were also readily ionized by the SCGD. Indeed, strong analyte signals were obtained from solid samples placed at least 2 cm from the plasma. These findings indicate that the SCGD might be useful also for ambient desorption/ionization mass spectrometry. Combined with earlier results that showed the SCGD is useful for ionization of labile biomolecules, the results here indicate that the SCGD is a highly versatile ion source capable of providing both elemental and molecular mass-spectral information. - Highlights: • Solution-cathode glow discharge used as an ionization source for mass spectrometry. • SCGD-MS can provide atomic as well as intact molecular mass spectra. • Atomic limits of detection range

  6. Quantification of the fluorine containing drug 5-fluorouracil in cancer cells by GaF molecular absorption via high-resolution continuum source molecular absorption spectrometry

    Science.gov (United States)

    Krüger, Magnus; Huang, Mao-Dong; Becker-Roß, Helmut; Florek, Stefan; Ott, Ingo; Gust, Ronald

    The development of high-resolution continuum source molecular absorption spectrometry made the quantification of fluorine feasible by measuring the molecular absorption as gallium monofluoride (GaF). Using this new technique, we developed on the example of 5-fluorouracil (5-FU) a graphite furnace method to quantify fluorine in organic molecules. The effect of 5-FU on the generation of the diatomic GaF molecule was investigated. The experimental conditions such as gallium nitrate amount, temperature program, interfering anions (represented as corresponding acids) and calibration for the determination of 5-FU in standard solution and in cellular matrix samples were investigated and optimized. The sample matrix showed no effect on the sensitivity of GaF molecular absorption. A simple calibration curve using an inorganic sodium fluoride solution can conveniently be used for the calibration. The described method is sensitive and the achievable limit of detection is 0.23 ng of 5-FU. In order to establish the concept of "fluorine as a probe in medicinal chemistry" an exemplary application was selected, in which the developed method was successfully demonstrated by performing cellular uptake studies of the 5-FU in human colon carcinoma cells.

  7. Quantification of the fluorine containing drug 5-fluorouracil in cancer cells by GaF molecular absorption via high-resolution continuum source molecular absorption spectrometry

    International Nuclear Information System (INIS)

    Krüger, Magnus; Huang, Mao-Dong; Becker-Roß, Helmut; Florek, Stefan; Ott, Ingo; Gust, Ronald

    2012-01-01

    The development of high-resolution continuum source molecular absorption spectrometry made the quantification of fluorine feasible by measuring the molecular absorption as gallium monofluoride (GaF). Using this new technique, we developed on the example of 5-fluorouracil (5-FU) a graphite furnace method to quantify fluorine in organic molecules. The effect of 5-FU on the generation of the diatomic GaF molecule was investigated. The experimental conditions such as gallium nitrate amount, temperature program, interfering anions (represented as corresponding acids) and calibration for the determination of 5-FU in standard solution and in cellular matrix samples were investigated and optimized. The sample matrix showed no effect on the sensitivity of GaF molecular absorption. A simple calibration curve using an inorganic sodium fluoride solution can conveniently be used for the calibration. The described method is sensitive and the achievable limit of detection is 0.23 ng of 5-FU. In order to establish the concept of “fluorine as a probe in medicinal chemistry” an exemplary application was selected, in which the developed method was successfully demonstrated by performing cellular uptake studies of the 5-FU in human colon carcinoma cells. - Highlights: ► Development of HR-CS MAS for quantification of fluorine bound to organic molecules ► Measuring as molecular absorption of gallium monofluoride ► Quantification of organic-bound fluorine in biological material ► The concept of “fluorine as a probe in medicinal chemistry” could be established

  8. Quantification of the fluorine containing drug 5-fluorouracil in cancer cells by GaF molecular absorption via high-resolution continuum source molecular absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Krueger, Magnus [Freie Universitaet Berlin, Institut fuer Pharmazie, Pharmazeutische Chemie, Koenigin-Luise-Str. 2-4, 14195 Berlin (Germany); Huang, Mao-Dong; Becker-Ross, Helmut; Florek, Stefan [Leibniz Institut fuer Analytische Wissenschaften, ISAS-e.V., Department Berlin, Albert-Einstein-Str. 9, 12489 Berlin (Germany); Ott, Ingo [Technische Universitaet Carolo Wilhelmina zu Braunschweig, Institut fuer Medizinische und Pharmazeutische Chemie, Beethovenstr. 55, 38106 Braunschweig (Germany); Gust, Ronald, E-mail: ronald.gust@uibk.ac.at [Universitaet Innsbruck, Institut fuer Pharmazie, Pharmazeutische Chemie, Innrain 80/82, 6020 Innsbruck (Austria)

    2012-03-15

    The development of high-resolution continuum source molecular absorption spectrometry made the quantification of fluorine feasible by measuring the molecular absorption as gallium monofluoride (GaF). Using this new technique, we developed on the example of 5-fluorouracil (5-FU) a graphite furnace method to quantify fluorine in organic molecules. The effect of 5-FU on the generation of the diatomic GaF molecule was investigated. The experimental conditions such as gallium nitrate amount, temperature program, interfering anions (represented as corresponding acids) and calibration for the determination of 5-FU in standard solution and in cellular matrix samples were investigated and optimized. The sample matrix showed no effect on the sensitivity of GaF molecular absorption. A simple calibration curve using an inorganic sodium fluoride solution can conveniently be used for the calibration. The described method is sensitive and the achievable limit of detection is 0.23 ng of 5-FU. In order to establish the concept of 'fluorine as a probe in medicinal chemistry' an exemplary application was selected, in which the developed method was successfully demonstrated by performing cellular uptake studies of the 5-FU in human colon carcinoma cells. - Highlights: Black-Right-Pointing-Pointer Development of HR-CS MAS for quantification of fluorine bound to organic molecules Black-Right-Pointing-Pointer Measuring as molecular absorption of gallium monofluoride Black-Right-Pointing-Pointer Quantification of organic-bound fluorine in biological material Black-Right-Pointing-Pointer The concept of 'fluorine as a probe in medicinal chemistry' could be established.

  9. Long-term monitoring of molecular markers can distinguish different seasonal patterns of fecal indicating bacteria sources.

    Science.gov (United States)

    Riedel, Timothy E; Thulsiraj, Vanessa; Zimmer-Faust, Amity G; Dagit, Rosi; Krug, Jenna; Hanley, Kaitlyn T; Adamek, Krista; Ebentier, Darcy L; Torres, Robert; Cobian, Uriel; Peterson, Sophie; Jay, Jennifer A

    2015-03-15

    Elevated levels of fecal indicator bacteria (FIB) have been observed at Topanga Beach, CA, USA. To identify the FIB sources, a microbial source tracking study using a dog-, a gull- and two human-associated molecular markers was conducted at 10 sites over 21 months. Historical data suggest that episodic discharge from the lagoon at the mouth of Topanga Creek is the main source of bacteria to the beach. A decline in creek FIB/markers downstream from upper watershed development and a sharp increase in FIB/markers at the lagoon sites suggest sources are local to the lagoon. At the lagoon and beach, human markers are detected sporadically, dog marker peaks in abundance mid-winter, and gull marker is chronically elevated. Varied seasonal patterns of FIB and source markers were identified showing the importance of applying a suite of markers over long-term spatial and temporal sampling to identify a complex combination of sources of contamination. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Molten Fluoride Salts as Fluorine Source in the Production of Molecular Sidebands

    CERN Document Server

    Shoaib, Maryam

    2015-01-01

    The medically important isotopes Yttrium and Zirconium were selected for fluorination. After this, 30 $\\mu$g of NaF as fluorine source was put in mass marker in the target unit. It was heated and plasma ion source was used to ionize the vapors. The ion source efficiency was 27\\%. It was observed that the yield for fluorine was not enough for various mass marker temperatures (0 A - 40 A) and ion source temperatures (2000 $^{o}$C - 2150$^{o}$C) to be reacted with other elements. The optimum temperatures of mass marker was observed here as 35 A. The project can be proceeded for further high temperatures and for different fluorine sources.

  11. Feasibility of high-resolution continuum source molecular absorption spectrometry in flame and furnace for sulphur determination in petroleum products

    Science.gov (United States)

    Kowalewska, Zofia

    2011-07-01

    For the first time, high-resolution molecular absorption spectrometry with a high-intensity xenon lamp as radiation source has been applied for the determination of sulphur in crude oil and petroleum products. The samples were analysed as xylene solutions using vaporisation in acetylene-air flame or in an electrothermally heated graphite furnace. The sensitive rotational lines of the CS molecule, belonging to the ∆ν = 0 vibrational sequence within the electronic transition X 1∑ + → A 1П, were applied. For graphite furnace molecular absorption spectrometry, the Pd + Mg organic modifier was selected. Strong interactions with Pd atoms enable easier decomposition of sulphur-containing compounds, likely through the temporal formation of Pd xS y molecules. At the 258.056 nm line, with the wavelength range covering central pixel ± 5 pixels and with application of interactive background correction, the detection limit was 14 ng in graphite furnace molecular absorption spectrometry and 18 mg kg -1 in flame molecular absorption spectrometry. Meanwhile, application of 2-points background correction found a characteristic mass of 12 ng in graphite furnace molecular absorption spectrometry and a characteristic concentration of 104 mg kg -1 in flame molecular absorption spectrometry. The range of application of the proposed methods turned out to be significantly limited by the properties of the sulphur compounds of interest. In the case of volatile sulphur compounds, which can be present in light petroleum products, severe difficulties were encountered. On the contrary, heavy oils and residues from distillation as well as crude oil could be analysed using both flame and graphite furnace vaporisation. The good accuracy of the proposed methods for these samples was confirmed by their mutual consistency and the results from analysis of reference samples (certified reference materials and home reference materials with sulphur content determined by X-ray fluorescence

  12. Feasibility of high-resolution continuum source molecular absorption spectrometry in flame and furnace for sulphur determination in petroleum products

    Energy Technology Data Exchange (ETDEWEB)

    Kowalewska, Zofia, E-mail: zofia.kowalewska@obr.pl

    2011-07-15

    For the first time, high-resolution molecular absorption spectrometry with a high-intensity xenon lamp as radiation source has been applied for the determination of sulphur in crude oil and petroleum products. The samples were analysed as xylene solutions using vaporisation in acetylene-air flame or in an electrothermally heated graphite furnace. The sensitive rotational lines of the CS molecule, belonging to the {Delta}{nu} = 0 vibrational sequence within the electronic transition X{sup 1}{Sigma}{sup +} {yields} A{sup 1}{Pi}, were applied. For graphite furnace molecular absorption spectrometry, the Pd + Mg organic modifier was selected. Strong interactions with Pd atoms enable easier decomposition of sulphur-containing compounds, likely through the temporal formation of Pd{sub x}S{sub y} molecules. At the 258.056 nm line, with the wavelength range covering central pixel {+-} 5 pixels and with application of interactive background correction, the detection limit was 14 ng in graphite furnace molecular absorption spectrometry and 18 mg kg{sup -1} in flame molecular absorption spectrometry. Meanwhile, application of 2-points background correction found a characteristic mass of 12 ng in graphite furnace molecular absorption spectrometry and a characteristic concentration of 104 mg kg{sup -1} in flame molecular absorption spectrometry. The range of application of the proposed methods turned out to be significantly limited by the properties of the sulphur compounds of interest. In the case of volatile sulphur compounds, which can be present in light petroleum products, severe difficulties were encountered. On the contrary, heavy oils and residues from distillation as well as crude oil could be analysed using both flame and graphite furnace vaporisation. The good accuracy of the proposed methods for these samples was confirmed by their mutual consistency and the results from analysis of reference samples (certified reference materials and home reference materials with

  13. Sources

    International Nuclear Information System (INIS)

    Duffy, L.P.

    1991-01-01

    This paper discusses the sources of radiation in the narrow perspective of radioactivity and the even narrow perspective of those sources that concern environmental management and restoration activities at DOE facilities, as well as a few related sources. Sources of irritation, Sources of inflammatory jingoism, and Sources of information. First, the sources of irritation fall into three categories: No reliable scientific ombudsman to speak without bias and prejudice for the public good, Technical jargon with unclear definitions exists within the radioactive nomenclature, and Scientific community keeps a low-profile with regard to public information. The next area of personal concern are the sources of inflammation. This include such things as: Plutonium being described as the most dangerous substance known to man, The amount of plutonium required to make a bomb, Talk of transuranic waste containing plutonium and its health affects, TMI-2 and Chernobyl being described as Siamese twins, Inadequate information on low-level disposal sites and current regulatory requirements under 10 CFR 61, Enhanced engineered waste disposal not being presented to the public accurately. Numerous sources of disinformation regarding low level radiation high-level radiation, Elusive nature of the scientific community, The Federal and State Health Agencies resources to address comparative risk, and Regulatory agencies speaking out without the support of the scientific community

  14. A ROTATING MOLECULAR DISK TOWARD IRAS 18162-2048, THE EXCITING SOURCE OF HH 80-81

    International Nuclear Information System (INIS)

    Fernandez-Lopez, M.; Curiel, S.; Girart, J. M.; Gomez, Y.; Ho, P. T. P.; Patel, N.

    2011-01-01

    We present several molecular line emission arcsecond and subarcsecond observations obtained with the Submillimeter Array in the direction of the massive protostar IRAS 18162-2048, the exciting source of HH 80-81. The data clearly indicate the presence of a compact (radius ∼425-850 AU) SO 2 structure, enveloping the more compact (radius ∼ sun . The SO 2 spectral line data also allow us to constrain the structure temperature between 120 and 160 K and the volume density ∼> 2 x 10 9 cm -3 . We also find that such a rotating flattened system could be unstable due to gravitational disturbances. The data from C 17 O line emission show a dense core within this star-forming region. Additionally, the H 2 CO and SO emissions appear clumpy and trace the disk-like structure, a possible interaction between a molecular core and the outflows, and in part, the cavity walls excavated by the thermal radio jet.

  15. Kinetics of Low Temperature Polyester Dyeing with High Molecular Weight Disperse Dyes by Solvent Microemulsion and AgroSourced Auxiliaries

    OpenAIRE

    Shahram Radei; F. Javier Carrión-Fité; Mònica Ardanuy; José María Canal

    2018-01-01

    This work focused on the evaluation of the kinetics of dyeing polyester fabrics with high molecular weight disperse dyes, at low temperature by solvent microemulsion. This study also compared the effect of two non-toxic agro-sourced auxiliaries (o-vanillin and coumarin) using a non-toxic organic solvent. A dyeing bath consisting of a micro-emulsion system involving a small proportion of n-butyl acetate was used, and the kinetics of dyeing were analysed at four temperatures (83, 90, 95 and 100...

  16. Growth kinetics and properties of ZnO/ZnMgO heterostructures grown by radical-source molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Ivanov, S.V. [Institute of Semiconductor Technology, Technical University Braunschweig, Hans-Sommer-Str. 66, 38106 Braunschweig (Germany); Ioffe Physico-Technical Institute, Polytekhnicheskaya Street 26, 194021 St. Petersburg (Russian Federation); El-Shaer, A.; Bakin, A.; Waag, A. [Institute of Semiconductor Technology, Technical University Braunschweig, Hans-Sommer-Str. 66, 38106 Braunschweig (Germany); Shubina, T.V.; Listoshin, S.B. [Ioffe Physico-Technical Institute, Polytekhnicheskaya Street 26, 194021 St. Petersburg (Russian Federation)

    2007-07-01

    A phenomenological approach to quantitative description of Zn(Mg)O growth by radical-source molecular beam epitaxy, based on the experimental studies of RHEED intensity oscillations, has been developed. It allows a precise control of growth rate, composition and stoichiometry at any growth temperature, Along with optimization of a growth initiation procedure on a c-sapphire, it is necessary condition for fabrication of high quality ZnO epilayers and ZnO/ZnMgO heterostructures in a wide Mg composition range. (copyright 2007 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  17. sources

    Directory of Open Access Journals (Sweden)

    Shu-Yin Chiang

    2002-01-01

    Full Text Available In this paper, we study the simplified models of the ATM (Asynchronous Transfer Mode multiplexer network with Bernoulli random traffic sources. Based on the model, the performance measures are analyzed by the different output service schemes.

  18. CMG-Biotools, a Free Workbench for Basic Comparative Microbial Genomics

    DEFF Research Database (Denmark)

    Vesth, Tammi Camilla; Lagesen, Karin; Acar, Öncel

    2013-01-01

    This paper shows the strength and diverse use of the CMG-biotools system. The system can be installed on a vide range of host operating systems and utilizes as much of the host computer as desired. It allows the user to compare multiple genomes, from various sources using standardized data formats...

  19. Metrological-grade tunable coherent source in the mid-infrared for molecular precision spectroscopy

    Science.gov (United States)

    Insero, G.; Clivati, C.; D'Ambrosio, D.; Cancio Pastor, P.; Verde, M.; Schunemann, P. G.; Zondy, J.-J.; Inguscio, M.; Calonico, D.; Levi, F.; De Natale, P.; Santambrogio, G.; Borri, S.

    2018-02-01

    We report on a metrological-grade mid-IR source with a 10-14 short-term instability for high-precision spectroscopy. Our source is based on the combination of a quantum cascade laser and a coherent radiation obtained by difference-frequency generation in an orientation-patterned gallium phosphide (OP-GaP) crystal. The pump and signal lasers are locked to an optical frequency comb referenced to the primary frequency standard via an optical fiber link. We demonstrate the robustness of the apparatus by measuring a vibrational transition around 6 μm on a metastable state of CO molecuels with 11 digits of precision.

  20. Molecular depth profiling of multi-layer systems with cluster ion sources

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Juan [Department of Chemistry, Penn State University, University Park, PA 16802 (United States); Winograd, Nicholas [Department of Chemistry, Penn State University, University Park, PA 16802 (United States)]. E-mail: nxw@psu.edu

    2006-07-30

    Cluster bombardment of molecular films has created new opportunities for SIMS research. To more quantitatively examine the interaction of cluster beams with organic materials, we have developed a reproducible platform consisting of a well-defined sugar film (trehalose) doped with peptides. Molecular depth profiles have been acquired with these systems using C{sub 60} {sup +} bombardment. In this study, we utilize this platform to determine the feasibility of examining buried interfaces for multi-layer systems. Using C{sub 60} {sup +} at 20 keV, several systems have been tested including Al/trehalose/Si, Al/trehalose/Al/Si, Ag/trehalose/Si and ice/trehalose/Si. The results show that there can be interactions between the layers during the bombardment process that prevent a simple interpretation of the depth profile. We find so far that the best results are obtained when the mass of the overlayer atoms is less than or nearly equal to the mass of the atoms in buried molecules. In general, these observations suggest that C{sub 60} {sup +} bombardment can be successfully applied to interface characterization of multi-layer systems if the systems are carefully chosen.

  1. Development and Evaluation of an Open-Source Software Package “CGITA” for Quantifying Tumor Heterogeneity with Molecular Images

    Directory of Open Access Journals (Sweden)

    Yu-Hua Dean Fang

    2014-01-01

    Full Text Available Background. The quantification of tumor heterogeneity with molecular images, by analyzing the local or global variation in the spatial arrangements of pixel intensity with texture analysis, possesses a great clinical potential for treatment planning and prognosis. To address the lack of available software for computing the tumor heterogeneity on the public domain, we develop a software package, namely, Chang-Gung Image Texture Analysis (CGITA toolbox, and provide it to the research community as a free, open-source project. Methods. With a user-friendly graphical interface, CGITA provides users with an easy way to compute more than seventy heterogeneity indices. To test and demonstrate the usefulness of CGITA, we used a small cohort of eighteen locally advanced oral cavity (ORC cancer patients treated with definitive radiotherapies. Results. In our case study of ORC data, we found that more than ten of the current implemented heterogeneity indices outperformed SUVmean for outcome prediction in the ROC analysis with a higher area under curve (AUC. Heterogeneity indices provide a better area under the curve up to 0.9 than the SUVmean and TLG (0.6 and 0.52, resp.. Conclusions. CGITA is a free and open-source software package to quantify tumor heterogeneity from molecular images. CGITA is available for free for academic use at http://code.google.com/p/cgita.

  2. Molecular detection of Fasciola hepatica in water sources of District Nowshehra Khyber Pakhtunkhwa Pakistan

    Science.gov (United States)

    Khan, Imran; Khan, Amir Muhammad; Ayaz, Khan, Sanaullah; Anees, Muhammad; Khan, Shaukat Ali

    2012-12-01

    Fascioliasis is spread through contamination of water sources and cause morbidity throughout the world. In the current study 300 water samples were processed by PCR for detection of Fasciola hepatica. The overall prevalence in different water sources was 9.66 % (29/300). Highest prevalence was recorded in drain water16 % (16/100) followed by tube well water 10% (4/40), open well water 8 % (8/100) and the lowest was recorded in tap water 1.66 %(1/60). The significant difference P < 0.05 was recorded during data analysis. The highest prevalence was recorded in summer. It was concluded from the study that cleaning and filtration should be adopted to avoid the health hazards against water borne zoonotic parasites.

  3. CMG-biotools, a free workbench for basic comparative microbial genomics.

    Science.gov (United States)

    Vesth, Tammi; Lagesen, Karin; Acar, Öncel; Ussery, David

    2013-01-01

    Today, there are more than a hundred times as many sequenced prokaryotic genomes than were present in the year 2000. The economical sequencing of genomic DNA has facilitated a whole new approach to microbial genomics. The real power of genomics is manifested through comparative genomics that can reveal strain specific characteristics, diversity within species and many other aspects. However, comparative genomics is a field not easily entered into by scientists with few computational skills. The CMG-biotools package is designed for microbiologists with limited knowledge of computational analysis and can be used to perform a number of analyses and comparisons of genomic data. The CMG-biotools system presents a stand-alone interface for comparative microbial genomics. The package is a customized operating system, based on Xubuntu 10.10, available through the open source Ubuntu project. The system can be installed on a virtual computer, allowing the user to run the system alongside any other operating system. Source codes for all programs are provided under GNU license, which makes it possible to transfer the programs to other systems if so desired. We here demonstrate the package by comparing and analyzing the diversity within the class Negativicutes, represented by 31 genomes including 10 genera. The analyses include 16S rRNA phylogeny, basic DNA and codon statistics, proteome comparisons using BLAST and graphical analyses of DNA structures. This paper shows the strength and diverse use of the CMG-biotools system. The system can be installed on a vide range of host operating systems and utilizes as much of the host computer as desired. It allows the user to compare multiple genomes, from various sources using standardized data formats and intuitive visualizations of results. The examples presented here clearly shows that users with limited computational experience can perform complicated analysis without much training.

  4. An open source digital servo for atomic, molecular, and optical physics experiments

    Energy Technology Data Exchange (ETDEWEB)

    Leibrandt, D. R., E-mail: david.leibrandt@nist.gov; Heidecker, J. [National Institute of Standards and Technology, Boulder, Colorado 80305 (United States)

    2015-12-15

    We describe a general purpose digital servo optimized for feedback control of lasers in atomic, molecular, and optical physics experiments. The servo is capable of feedback bandwidths up to roughly 1 MHz (limited by the 320 ns total latency); loop filter shapes up to fifth order; multiple-input, multiple-output control; and automatic lock acquisition. The configuration of the servo is controlled via a graphical user interface, which also provides a rudimentary software oscilloscope and tools for measurement of system transfer functions. We illustrate the functionality of the digital servo by describing its use in two example scenarios: frequency control of the laser used to probe the narrow clock transition of {sup 27}Al{sup +} in an optical atomic clock, and length control of a cavity used for resonant frequency doubling of a laser.

  5. kspectrum: an open-source code for high-resolution molecular absorption spectra production

    International Nuclear Information System (INIS)

    Eymet, V.; Coustet, C.; Piaud, B.

    2016-01-01

    We present the kspectrum, scientific code that produces high-resolution synthetic absorption spectra from public molecular transition parameters databases. This code was originally required by the atmospheric and astrophysics communities, and its evolution is now driven by new scientific projects among the user community. Since it was designed without any optimization that would be specific to any particular application field, its use could also be extended to other domains. kspectrum produces spectral data that can subsequently be used either for high-resolution radiative transfer simulations, or for producing statistic spectral model parameters using additional tools. This is a open project that aims at providing an up-to-date tool that takes advantage of modern computational hardware and recent parallelization libraries. It is currently provided by Méso-Star (http://www.meso-star.com) under the CeCILL license, and benefits from regular updates and improvements. (paper)

  6. An open source digital servo for atomic, molecular, and optical physics experiments

    Science.gov (United States)

    Leibrandt, D. R.; Heidecker, J.

    2015-12-01

    We describe a general purpose digital servo optimized for feedback control of lasers in atomic, molecular, and optical physics experiments. The servo is capable of feedback bandwidths up to roughly 1 MHz (limited by the 320 ns total latency); loop filter shapes up to fifth order; multiple-input, multiple-output control; and automatic lock acquisition. The configuration of the servo is controlled via a graphical user interface, which also provides a rudimentary software oscilloscope and tools for measurement of system transfer functions. We illustrate the functionality of the digital servo by describing its use in two example scenarios: frequency control of the laser used to probe the narrow clock transition of 27Al+ in an optical atomic clock, and length control of a cavity used for resonant frequency doubling of a laser.

  7. An open source digital servo for atomic, molecular, and optical physics experiments

    International Nuclear Information System (INIS)

    Leibrandt, D. R.; Heidecker, J.

    2015-01-01

    We describe a general purpose digital servo optimized for feedback control of lasers in atomic, molecular, and optical physics experiments. The servo is capable of feedback bandwidths up to roughly 1 MHz (limited by the 320 ns total latency); loop filter shapes up to fifth order; multiple-input, multiple-output control; and automatic lock acquisition. The configuration of the servo is controlled via a graphical user interface, which also provides a rudimentary software oscilloscope and tools for measurement of system transfer functions. We illustrate the functionality of the digital servo by describing its use in two example scenarios: frequency control of the laser used to probe the narrow clock transition of 27 Al + in an optical atomic clock, and length control of a cavity used for resonant frequency doubling of a laser

  8. Quantitative study of luminescence optical tomography. Application to sources localisation in molecular imaging

    International Nuclear Information System (INIS)

    Boffety, Matthieu

    2010-01-01

    Molecular imaging is a major modality in the field of preclinical research. Among the existing methods, techniques based on optical detection of visible or near infrared radiation are the most recent and are mainly represented by luminescence optical tomography techniques. These methods allow for 3D characterization of a biological medium by reconstructing maps of concentration or localisation of luminescent beacons sensitive to biological and chemical processes at the molecular or cellular scale. Luminescence optical tomography is based on a model of light propagation in tissues, a protocol for acquiring surface signal and a numerical inversion procedure used to reconstruct the parameters of interest. This thesis is structured around these three axes and provides an answer to each problem. The main objective of this study is to introduce and present the tools to evaluate the theoretical performances of optical tomography methods. One of its major outcomes is the realisation of experimental tomographic reconstructions from images acquired by an optical imager designed for 2D planar imaging and developed by the company Quidd. In a first step we develop the theory of transport in scattering medium to establish the concept on which our work will rely. We present two different propagation models as well as resolution methods and theoretical difficulties associated with them. In a second part we introduce the statistical tools used to characterise tomographic systems. We define and apply a procedure to simple situations in luminescence optical tomography. The last part of this work presents the development of an inversion procedure. After introducing the theoretical framework we validate the procedure from numerical data before successfully applying it to experimental measurements. (author) [fr

  9. Molecular beam (1-50eV) production by duoplasmatron source

    International Nuclear Information System (INIS)

    Delmas, M.; Gautherin, G.; Lejeune, C.

    1974-01-01

    The duoplasmatron discharge is commonly used to produce intense ion beams. A theoretical model of this discharge has been previously developed. The analysis of charge exchange processes between ions and neutral within the discharge shows that the source is able to deliver intense neutral beams (10 16 part s -1 ), the energy being in the range 1-50 eV. The intensity and energy distribution may be controlled from the discharge parameter variations. An experimental device has been realized in order to separate the neutral beam and the flux of charged particles; these latter are injected axially in a toroidal magnetic field configuration [fr

  10. Heat sources for bright-rimmed molecular clouds: CO observations of NGC 7822

    International Nuclear Information System (INIS)

    Elmegreen, B.G.; Dickinson, D.F.; Lada, C.J.

    1978-01-01

    Observations of the 2.6 mm carbon monoxide line in the bright rim NGC 7822 reveal that the peak excitation and column density of the molecule lie in a ridge ahead of the ionization front. Several possibilities for the excitation of this ridge are discussed. Cosmic rays are shown to provide an excellent heat source for Bok globules, but they can account for only approx.20% of the required heating in NGC 7822. Direct shock or compressional heating of the gas could be adequate only if the pressure inside the cloud is much larger than the thermal pressure. If, in fact, this internal pressure is determined by the source of line broadening (e.g., magnetic fields or turbulence), then shock or compressional heating could be important, and pressure equilibrium may exist between the neutral cloud and the bright rim. Heating by warm grains or by the photoelectric effect is also considered, but such mechanisms are probably not important if the only source of radiation is external to the cloud. This is primarily a result of the low cloud density (approx.10 3 cm -3 ) inferred from our observations. The extent to which unknown embedded stars may provide the required gaseous heating cannot be estimated from our observations of NGC 7822.An interesting and new heat source is suggested which may have important applications to bright-rimmed clouds or to any other predominantly neutral clouds that may have undergone some recent compression. We suggest that the heat input to neutral gas due to the relaxation of internal magnetic fields will be greatly enhanced during cloud compression (with or without a shock). We show that the power input to the gas will increase more with increasing density than will the cooling rate. As a result, cloud compression can lead to an increase in the gas temperature for a period lasting several million years, which is the decay time of the compressed field. The observed ridge in NGC 7822 may be due to stimulated release of internal magnetic energy

  11. Gas Source Techniques for Molecular Beam Epitaxy of Highly Mismatched Ge Alloys

    OpenAIRE

    Chad A. Stephenson; Miriam Gillett-Kunnath; William A. O’Brien; Robert Kudrawiec; Mark A. Wistey

    2016-01-01

    Ge and its alloys are attractive candidates for a laser compatible with silicon integrated circuits. Dilute germanium carbide (Ge1−xCx) offers a particularly interesting prospect. By using a precursor gas with a Ge4C core, C can be preferentially incorporated in substitutional sites, suppressing interstitial and C cluster defects. We present a method of reproducible and upscalable gas synthesis of tetrakis(germyl)methane, or (H3Ge)4C, followed by the design of a hybrid gas/solid-source molecu...

  12. Prediction With Dimension Reduction of Multiple Molecular Data Sources for Patient Survival

    Directory of Open Access Journals (Sweden)

    Adam Kaplan

    2017-07-01

    Full Text Available Predictive modeling from high-dimensional genomic data is often preceded by a dimension reduction step, such as principal component analysis (PCA. However, the application of PCA is not straightforward for multisource data, wherein multiple sources of ‘omics data measure different but related biological components. In this article, we use recent advances in the dimension reduction of multisource data for predictive modeling. In particular, we apply exploratory results from Joint and Individual Variation Explained (JIVE, an extension of PCA for multisource data, for prediction of differing response types. We conduct illustrative simulations to illustrate the practical advantages and interpretability of our approach. As an application example, we consider predicting survival for patients with glioblastoma multiforme from 3 data sources measuring messenger RNA expression, microRNA expression, and DNA methylation. We also introduce a method to estimate JIVE scores for new samples that were not used in the initial dimension reduction and study its theoretical properties; this method is implemented in the R package R.JIVE on CRAN, in the function jive.predict.

  13. Source Apportionment of Background PAHs in the Peace-Athabasca Delta (Alberta, Canada) Using Molecular Level Radiocarbon Analysis.

    Science.gov (United States)

    Jautzy, Josué J; Ahad, Jason M E; Hall, Roland I; Wiklund, Johan A; Wolfe, Brent B; Gobeil, Charles; Savard, Martine M

    2015-08-04

    The downstream accumulation of polycyclic aromatic hydrocarbons (PAHs) in the Peace-Athabasca Delta (PAD), an ecologically important landscape, is a key issue of concern given the rapid development of the oil sands industry in Northern Alberta, Canada. In addition to PAHs derived from industrial activity (i.e., oil sands mining) within the Athabasca watershed, however, forest fires and erosion of fossil fuel deposits within both the Athabasca and Peace watersheds are two potentially important natural sources of PAHs delivered to the PAD. Consequently, evaluating the environmental impact of mining activities requires a quantitative understanding of natural, background PAHs. Here, we utilize molecular-level natural-abundance radiocarbon measurements on an amalgamated sediment record from a Peace River flood-susceptible oxbow lake in the northern Peace sector of the PAD to quantitatively discriminate sources of naturally occurring alkylated PAHs (fossil and modern biomass). A radiocarbon mass balance quantified a predominantly natural petrogenic source (93% petrogenic, 7% forest fire) for alkylated PAHs during the past ∼50 years. Additionally, a significant petrogenic component determined for retene, a compound usually considered a biomarker for softwood combustion, suggests that its use as a unique forest fire indicator may not be suitable in PAD sediments receiving Peace watershed-derived fluvial inputs.

  14. GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit

    Energy Technology Data Exchange (ETDEWEB)

    Pronk, Sander [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Pall, Szilard [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Schulz, Roland [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Larsson, Per [Univ. of Virginia, Charlottesville, VA (United States); Bjelkmar, Par [Science for Life Lab., Stockholm (Sweden); Stockholm Univ., Stockholm (Sweden); Apostolov, Rossen [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Shirts, Michael R. [Univ. of Virginia, Charlottesville, VA (United States); Smith, Jeremy C. [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Kasson, Peter M. [Univ. of Virginia, Charlottesville, VA (United States); van der Spoel, David [Science for Life Lab., Stockholm (Sweden); Uppsala Univ., Uppsala (Sweden); Hess, Berk [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Lindahl, Erik [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Stockholm Univ., Stockholm (Sweden)

    2013-02-13

    In this study, molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. As a result, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.

  15. Radical-source molecular beam epitaxy of ZnO-based heterostructures

    Energy Technology Data Exchange (ETDEWEB)

    Sadofiev, Sergey

    2009-10-27

    This work focuses on the development of the novel growth approaches for the fabrication of Group II-oxide materials in the form of epitaxial films and heterostructures. It is shown that molecular-beam epitaxial growth far from thermal equilibrium allows one to overcome the standard solubility limit and to alloy ZnO with MgO or CdO in strict wurtzite phase up to mole fractions of several 10 %. In this way, a band-gap range from 2.2 to 4.4 eV can be covered. A clear layer-by-layer growth mode controlled by oscillations in reflection high-energy electron diffraction makes it possible to fabricate atomically smooth heterointerfaces and well-defined quantum well structures exhibiting prominent band-gap related light emission in the whole composition range. On appropriately designed structures, laser action from the ultraviolet down to green wavelengths and up to room temperature is achieved. The properties and potential of the ''state-of-the-art'' materials are discussed in relation to the advantages for their applications in various optoelectronic devices. (orig.)

  16. Dietary carbohydrate source influences molecular fingerprints of the rat faecal microbiota

    DEFF Research Database (Denmark)

    Licht, Tine Rask; Hansen, Max; Poulsen, Morten

    2006-01-01

    Background: A study was designed to elucidate effects of selected carbohydrates on composition and activity of the intestinal microbiota. Five groups of eight rats were fed a western type diet containing cornstarch (reference group), sucrose, potato starch, inulin (a long-chained fructan) or olig......Background: A study was designed to elucidate effects of selected carbohydrates on composition and activity of the intestinal microbiota. Five groups of eight rats were fed a western type diet containing cornstarch (reference group), sucrose, potato starch, inulin (a long-chained fructan...... of coliform bacteria in faeces. In the inulin and oligofructose groups, higher levels of butyrate and propionate, respectively, were measured. Principal Component Analysis of profiles of the faecal microbiota obtained by Denaturing Gradient Gel Electrophoresis (DGGE) of PCR amplified bacterial 16S rRNA genes...... and are not expected to reach the large intestine, the DGGE band patterns obtained indicated that these carbohydrates indeed affected the composition of bacteria in the large gut. Also the two fructans resulted in completely different molecular fingerprints of the faecal microbiota, indicating that even though...

  17. Molecular epidemiology of nontuberculous mycobacteria isolates from clinical and environmental sources of a metropolitan city.

    Science.gov (United States)

    Velayati, Ali Akbar; Farnia, Parissa; Mozafari, Mohadese; Malekshahian, Donya; Seif, Shima; Rahideh, Snaz; Mirsaeidi, Mehdi

    2014-01-01

    While NTM infection is mainly acquired from environmental exposure, monitoring of environmental niches for NTM is not a routine practice. This study aimed to find the prevalence of environmental NTM in soil and water in four highly populated suburbs of Tehran, Iran. A total of 4014 samples from soil and water resources were collected and studied. Sediments of each treated sample were cultured in Lowenstein-Jensen medium and observed twice per week for growth rate, colony morphology, and pigmentation. Colonies were studied with phenotypic tests. Molecular analysis was performed on single colonies derived from subculture of original isolates. Environmental samples were compared with 34 NTM isolates from patients who were residents of the study locations. Out of 4014 samples, mycobacteria were isolated from 862 (21.4%) specimens; 536 (62.1%) belonged to slow growing mycobacteria (SGM) and 326 (37.8%) were rapid growing mycobacteria (RGM). The five most frequent NTM were M. farcinogens (105/862; 12.1%), M. fortuitum (72/862; 8.3%), M. senegalense (58/862; 6.7%), M. kansasii (54/862; 6.2%), and M. simiae (46/862; 5.3%). In total, 62.5% (539/862) of mycobacterial positive samples were isolated from water and only 37.4% (323/862) of them were isolated from soil samples (Pdistribution pattern of environmental NTM isolates with clinical isolates suggests a possible transmission link, but this does not apply to all environmental NTM species. Our study confirms an increasing trend of NTM isolation from clinical samples that needs further investigation.

  18. Bringing high-performance computing to the biologist's workbench: approaches, applications, and challenges

    International Nuclear Information System (INIS)

    Oehmen, C S; Cannon, W R

    2008-01-01

    Data-intensive and high-performance computing are poised to significantly impact the future of biological research which is increasingly driven by the prevalence of high-throughput experimental methodologies for genome sequencing, transcriptomics, proteomics, and other areas. Large centers such as NIH's National Center for Biotechnology Information, The Institute for Genomic Research, and the DOE's Joint Genome Institute) have made extensive use of multiprocessor architectures to deal with some of the challenges of processing, storing and curating exponentially growing genomic and proteomic datasets, thus enabling users to rapidly access a growing public data source, as well as use analysis tools transparently on high-performance computing resources. Applying this computational power to single-investigator analysis, however, often relies on users to provide their own computational resources, forcing them to endure the learning curve of porting, building, and running software on multiprocessor architectures. Solving the next generation of large-scale biology challenges using multiprocessor machines-from small clusters to emerging petascale machines-can most practically be realized if this learning curve can be minimized through a combination of workflow management, data management and resource allocation as well as intuitive interfaces and compatibility with existing common data formats

  19. The coupling of MATISSE and the SE-WORKBENCH: a new solution for simulating efficiently the atmospheric radiative transfer and the sea surface radiation

    Science.gov (United States)

    Cathala, Thierry; Douchin, Nicolas; Latger, Jean; Caillault, Karine; Fauqueux, Sandrine; Huet, Thierry; Lubarre, Luc; Malherbe, Claire; Rosier, Bernard; Simoneau, Pierre

    2009-05-01

    The SE-WORKBENCH workshop, also called CHORALE (French acceptation for "simulated Optronic Acoustic Radar battlefield") is used by the French DGA (MoD) and several other Defense organizations and companies all around the World to perform multi-sensors simulations. CHORALE enables the user to create virtual and realistic multi spectral 3D scenes that may contain several types of target, and then generate the physical signal received by a sensor, typically an IR sensor. The SE-WORKBENCH can be used either as a collection of software modules through dedicated GUIs or as an API made of a large number of specialized toolkits. The SE-WORKBENCH is made of several functional block: one for geometrically and physically modeling the terrain and the targets, one for building the simulation scenario and one for rendering the synthetic environment, both in real and non real time. Among the modules that the modeling block is composed of, SE-ATMOSPHERE is used to simulate the atmospheric conditions of a Synthetic Environment and then to integrate the impact of these conditions on a scene. This software product generates an exploitable physical atmosphere by the SE WORKBENCH tools generating spectral images. It relies on several external radiative transfer models such as MODTRAN V4.2 in the current version. MATISSE [4,5] is a background scene generator developed for the computation of natural background spectral radiance images and useful atmospheric radiative quantities (radiance and transmission along a line of sight, local illumination, solar irradiance ...). Backgrounds include atmosphere, low and high altitude clouds, sea and land. A particular characteristic of the code is its ability to take into account atmospheric spatial variability (temperatures, mixing ratio, etc) along each line of sight. An Application Programming Interface (API) is included to facilitate its use in conjunction with external codes. MATISSE is currently considered as a new external radiative transfer

  20. p-type ZnO films with solid-source phosphorus doping by molecular-beam epitaxy

    International Nuclear Information System (INIS)

    Xiu, F.X.; Yang, Z.; Mandalapu, L.J.; Liu, J.L.; Beyermann, W. P.

    2006-01-01

    Phosphorus-doped p-type ZnO films were grown on r-plane sapphire substrates using molecular-beam epitaxy with a solid-source GaP effusion cell. X-ray diffraction spectra and reflection high-energy electron diffraction patterns indicate that high-quality single crystalline (1120) ZnO films were obtained. Hall and resistivity measurements show that the phosphorus-doped ZnO films have high hole concentrations and low resistivities at room temperature. Photoluminescence (PL) measurements at 8 K reveal a dominant acceptor-bound exciton emission with an energy of 3.317 eV. The acceptor energy level of the phosphorus dopant is estimated to be 0.18 eV above the valence band from PL spectra, which is also consistent with the temperature dependence of PL measurements

  1. Contribution to the study of the molecular scattering of light. Use of a laser as light source (1963)

    International Nuclear Information System (INIS)

    Slama, L.

    1963-01-01

    The experiments of the molecular scattering of light have been repeated using a ruby laser as a light source. The angular distribution of the scattered light intensity has been measured when the electric vector of the incident beam is either in the plane of observation or perpendicular to that plane. In the first case a good agreement with the Rayleigh theory has been found but this is not true in the second case. The differential cross sections for scattering have been measured for various gases. The values found are two or three times larger than the ones deduced from the classical theory. The possible effect of a variation of the beam intensity upon the linearity of the scattering process has been looked for. (author) [fr

  2. Preparation and electrical properties of boron and boron phosphide films obtained by gas source molecular beam deposition

    Energy Technology Data Exchange (ETDEWEB)

    Kumashiro, Y.; Yokoyama, T.; Sakamoto, T.; Fujita, T. [Yokohama National Univ. (Japan)

    1997-10-01

    Boron and boron phosphide films were prepared by gas source molecular beam deposition on sapphire crystal at various substrate temperatures up to 800{degrees}C using cracked B{sub 2}H{sub 6} (2% in H{sub 2}) at 300{degrees}C and cracked PH{sub 3} (20% in H{sub 2}) at 900{degrees}C. The substrate temperatures and gas flow rates of the reactant gases determined the film growth. The boron films with amorphous structure are p type. Increasing growth times lead to increasing mobilities and decreasing carrier concentrations. Boron phosphide film with maximum P/B ratio is obtained at a substrate temperature of 600{degrees}C, below and above which they become phosphorous deficient due to insufficient supply of phosphorus and thermal desorption of the phosphorus as P{sub 2}, respectively, but they are all n type conductors due to phosphorus vacancies.

  3. Soft X-Ray Microscopy and Spectroscopy at the Molecular Environmental Science Beamline at the Advanced Light Source

    Energy Technology Data Exchange (ETDEWEB)

    Bluhm, Hendrik; Andersson, Klas J.; Araki, Tohru; Benzerara, Karim; Brown, Gordon E.; Dynes, Jay J.; Ghosal, Sutapa; Gilles, Mary K.; Hansen, Hans C.; Hemminger, J. C.; Hitchcock, Adam P.; Ketteler, Guido; Kilcoyne, Arthur L.; Kneedler, Eric M.; Lawrence, John R.; Leppard, Gary G.; Majzlam, Juraj; Mun, B. S.; Myneni, Satish C.; Nilsson, Anders R.; Ogasawara, Hirohito; Ogletree, D. F.; Pecher, Klaus H.; Salmeron, Miquel B.; Shuh, David K.; Tonner, Brian; Tyliszczak, Tolek; Warwick, Tony; Yoon, T. H.

    2006-02-01

    We present examples of the application of synchrotron-based spectroscopies and microscopies to environmentally-relevant samples. The experiments were performed at the Molecular Environmental Science beamline (11.0.2) at the Advanced Light Source, Lawrence Berkeley National Laboratory. Examples range from the study of water monolayers on Pt(111) single crystal surfaces using X-ray emission spectroscopy and the examination of alkali halide solution/water vapor interfaces using ambient pressure photoemission spectroscopy, to the investigation of actinides, river-water biofilms, Al-containing colloids and mineral-bacteria suspensions using scanning transmission X-ray spectromicroscopy. The results of our experiments show that spectroscopy and microscopy in the soft X-ray energy range are excellent tools for the investigation of environmentally relevant samples under realistic conditions, i.e. with water or water vapor present at ambient temperature.

  4. Argo: an integrative, interactive, text mining-based workbench supporting curation

    Science.gov (United States)

    Rak, Rafal; Rowley, Andrew; Black, William; Ananiadou, Sophia

    2012-01-01

    Curation of biomedical literature is often supported by the automatic analysis of textual content that generally involves a sequence of individual processing components. Text mining (TM) has been used to enhance the process of manual biocuration, but has been focused on specific databases and tasks rather than an environment integrating TM tools into the curation pipeline, catering for a variety of tasks, types of information and applications. Processing components usually come from different sources and often lack interoperability. The well established Unstructured Information Management Architecture is a framework that addresses interoperability by defining common data structures and interfaces. However, most of the efforts are targeted towards software developers and are not suitable for curators, or are otherwise inconvenient to use on a higher level of abstraction. To overcome these issues we introduce Argo, an interoperable, integrative, interactive and collaborative system for text analysis with a convenient graphic user interface to ease the development of processing workflows and boost productivity in labour-intensive manual curation. Robust, scalable text analytics follow a modular approach, adopting component modules for distinct levels of text analysis. The user interface is available entirely through a web browser that saves the user from going through often complicated and platform-dependent installation procedures. Argo comes with a predefined set of processing components commonly used in text analysis, while giving the users the ability to deposit their own components. The system accommodates various areas and levels of user expertise, from TM and computational linguistics to ontology-based curation. One of the key functionalities of Argo is its ability to seamlessly incorporate user-interactive components, such as manual annotation editors, into otherwise completely automatic pipelines. As a use case, we demonstrate the functionality of an in

  5. π Scope: python based scientific workbench with visualization tool for MDSplus data

    Science.gov (United States)

    Shiraiwa, S.

    2014-10-01

    π Scope is a python based scientific data analysis and visualization tool constructed on wxPython and Matplotlib. Although it is designed to be a generic tool, the primary motivation for developing the new software is 1) to provide an updated tool to browse MDSplus data, with functionalities beyond dwscope and jScope, and 2) to provide a universal foundation to construct interface tools to perform computer simulation and modeling for Alcator C-Mod. It provides many features to visualize MDSplus data during tokamak experiments including overplotting different signals and discharges, various plot types (line, contour, image, etc.), in-panel data analysis using python scripts, and publication quality graphics generation. Additionally, the logic to produce multi-panel plots is designed to be backward compatible with dwscope, enabling smooth migration for dwscope users. πScope uses multi-threading to reduce data transfer latency, and its object-oriented design makes it easy to modify and expand while the open source nature allows portability. A built-in tree data browser allows a user to approach the data structure both from a GUI and a script, enabling relatively complex data analysis workflow to be built quickly. As an example, an IDL-based interface to perform GENRAY/CQL3D simulations was ported on πScope, thus allowing LHCD simulation to be run between-shot using C-Mod experimental profiles. This workflow is being used to generate a large database to develop a LHCD actuator model for the plasma control system. Supported by USDoE Award DE-FC02-99ER54512.

  6. Determination of sulfur in coal and ash slurry by high-resolution continuum source electrothermal molecular absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Nakadi, Flávio V.; Rosa, Lilian R.; Veiga, Márcia A.M.S. da, E-mail: mamsveiga@ffclrp.usp.br

    2013-10-01

    We propose a procedure for the determination of sulfur in coal slurries by high resolution continuum source electrothermal molecular absorption spectrometry. The slurry, whose concentration is 1 mg mL{sup −1}, was prepared by mixing 50 mg of the sample with 5% v/v nitric acid and 0.04% m/v Triton X-100 and was homogenized manually. It sustained good stability. The determination was performed via CS molecular absorption at 257.592 nm, and the optimized vaporization temperature was 2500 °C. The accuracy of the method was ensured by analysis of certified reference materials SRM 1632b (trace elements in coal) and SRM 1633b (coal fly ash) from the National Institute of Standards and Technology, using external calibration with aqueous standards prepared in the same medium and used as slurry. We achieved good agreement with the certified reference materials within 95% confidence interval, LOD of 0.01% w/w, and RSD of 6%, which confirms the potential of the proposed method. - Highlights: • HR-CS ET MAS as a technique to determine sulfur in coal and ash • Utilization of (coal and coal fly ash) slurry as a sample preparation • Simple and fast method, which uses external calibration with aqueous standards without chemical modifier.

  7. Determination of total sulfur in agricultural samples by high-resolution continuum source flame molecular absorption spectrometry.

    Science.gov (United States)

    Virgilio, Alex; Raposo, Jorge L; Cardoso, Arnaldo A; Nóbrega, Joaquim A; Gomes Neto, José A

    2011-03-23

    The usefulness of molecular absorption was investigated for the determination of total sulfur (S) in agricultural samples by high-resolution continuum source flame molecular absorption spectrometry. The lines for CS at 257.595, 257.958, and 258.056 nm and for SH at 323.658, 324.064, and 327.990 nm were evaluated. Figures of merit, such as linear dynamic range, sensitivity, linear correlation, characteristic concentration, limit of detection, and precision, were established. For selected CS lines, wavelength-integrated absorbance equivalent to 3 pixels, analytical curves in the 100-2500 mg L(-1) (257.595 nm), 250-2000 mg L(-1) (257.958 nm), and 250-5000 mg L(-1) (258.056 nm) ranges with a linear correlation coefficient better than 0.9980 were obtained. Results were in agreement at a 95% confidence level (paired t test) with those obtained by gravimetry. Recoveries of S in fungicide and fertilizer samples were within the 84-109% range, and the relative standard deviation (n=12) was typically <5%.

  8. Determination of boron isotope ratios by high-resolution continuum source molecular absorption spectrometry using graphite furnace vaporizers

    Science.gov (United States)

    Abad, Carlos; Florek, Stefan; Becker-Ross, Helmut; Huang, Mao-Dong; Heinrich, Hans-Joachim; Recknagel, Sebastian; Vogl, Jochen; Jakubowski, Norbert; Panne, Ulrich

    2017-10-01

    Boron isotope amount ratios n(10B)/n(11B) have been determined by monitoring the absorption spectrum of boron monohydride (BH) in a graphite furnace using high-resolution continuum source molecular absorption spectrometry (HR-CS-MAS). Bands (0 → 0) and (1 → 1) for the electronic transition X1Σ+ → A1Π were evaluated around wavelengths 433.1 nm and 437.1 nm respectively. Clean and free of memory effect molecular spectra of BH were recorded. In order to eliminate the memory effect of boron, a combination of 2% (v/v) hydrogen gas in argon and 1% trifluoromethane in argon, an acid solution of calcium chloride and mannitol as chemical modifiers was used. Partial least square regression (PLS) for analysis of samples and reference materials were applied. For this, a spectral library with different isotopes ratios for PLS regression was built. Results obtained around the 433.1 nm and 437.1 nm spectral regions are metrologically compatible with those reported by mass spectrometric methods. Moreover, for the evaluated region of 437 nm, an accuracy of 0.15‰ is obtained as the average deviation from the isotope reference materials. Expanded uncertainties with a coverage factor of k = 2 range between 0.15 and 0.44‰. This accuracy and precision are compatible with those obtained by mass spectrometry for boron isotope ratio measurements.

  9. Determination of trace concentrations of chlorine in aqueous solutions by high-resolution continuum source graphite furnace molecular absorption spectrometry

    Science.gov (United States)

    Machyňák, Ľubomír; Čacho, František; Němeček, Martin; Beinrohr, Ernest

    2016-11-01

    Trace concentrations of total chlorine were determined by means of molecular absorption of indium mono-chloride (InCl) at 267.217 nm using high-resolution continuum source graphite furnace molecular absorption spectrometry. The effects of chemical modifiers and the amount of In on the sensitivity and accuracy were investigated. The optimum pyrolysis and vaporization temperatures were 600 °C and 1400 °C, respectively. The limit of detection and characteristic mass were found to be 0.10 ng and 0.21 ng, respectively. Potential non-spectral and spectral interferences were tested for various metals and non-metals at concentrations up to 50 mg L- 1 and for phosphoric, sulphuric and nitric acids. No spectral interferences were observed. Significant non-spectral interferences were observed with F, Br, and I at concentrations higher than 1 mg L- 1, 5 mg L- 1 and 25 mg L- 1, respectively, which is probably caused by formation of competitive indium halogen molecules. Higher concentrations of mineral acids depressed the signal owing to the formation of volatile HCl. The calibration curve was linear in the range between 0.3 and 10 ng with a correlation coefficient of R = 0.993. The elaborated method was used for the chlorine determination in various waters and a drug sample.

  10. Molecular property diagnostic suite (MPDS): Development of disease-specific open source web portals for drug discovery.

    Science.gov (United States)

    Nagamani, S; Gaur, A S; Tanneeru, K; Muneeswaran, G; Madugula, S S; Consortium, Mpds; Druzhilovskiy, D; Poroikov, V V; Sastry, G N

    2017-11-01

    Molecular property diagnostic suite (MPDS) is a Galaxy-based open source drug discovery and development platform. MPDS web portals are designed for several diseases, such as tuberculosis, diabetes mellitus, and other metabolic disorders, specifically aimed to evaluate and estimate the drug-likeness of a given molecule. MPDS consists of three modules, namely data libraries, data processing, and data analysis tools which are configured and interconnected to assist drug discovery for specific diseases. The data library module encompasses vast information on chemical space, wherein the MPDS compound library comprises 110.31 million unique molecules generated from public domain databases. Every molecule is assigned with a unique ID and card, which provides complete information for the molecule. Some of the modules in the MPDS are specific to the diseases, while others are non-specific. Importantly, a suitably altered protocol can be effectively generated for another disease-specific MPDS web portal by modifying some of the modules. Thus, the MPDS suite of web portals shows great promise to emerge as disease-specific portals of great value, integrating chemoinformatics, bioinformatics, molecular modelling, and structure- and analogue-based drug discovery approaches.

  11. Molecular epidemiology of nontuberculous mycobacteria isolates from clinical and environmental sources of a metropolitan city.

    Directory of Open Access Journals (Sweden)

    Ali Akbar Velayati

    Full Text Available While NTM infection is mainly acquired from environmental exposure, monitoring of environmental niches for NTM is not a routine practice. This study aimed to find the prevalence of environmental NTM in soil and water in four highly populated suburbs of Tehran, Iran.A total of 4014 samples from soil and water resources were collected and studied. Sediments of each treated sample were cultured in Lowenstein-Jensen medium and observed twice per week for growth rate, colony morphology, and pigmentation. Colonies were studied with phenotypic tests. Molecular analysis was performed on single colonies derived from subculture of original isolates. Environmental samples were compared with 34 NTM isolates from patients who were residents of the study locations.Out of 4014 samples, mycobacteria were isolated from 862 (21.4% specimens; 536 (62.1% belonged to slow growing mycobacteria (SGM and 326 (37.8% were rapid growing mycobacteria (RGM. The five most frequent NTM were M. farcinogens (105/862; 12.1%, M. fortuitum (72/862; 8.3%, M. senegalense (58/862; 6.7%, M. kansasii (54/862; 6.2%, and M. simiae (46/862; 5.3%. In total, 62.5% (539/862 of mycobacterial positive samples were isolated from water and only 37.4% (323/862 of them were isolated from soil samples (P<0.05. Out of 5314 positive clinical samples for mycobacteria, 175 (3.2% isolates were NTM. The trend of NTM isolates increased from 1.2% (13 out of 1078 in 2004 to 3.8% (39 out of 1005 in 2014 (P = 0.0001. The major clinical isolates were M. simiae (51; 29.1%, M. kansasii (26; 14.8%, M. chelonae (28; 16%, and M. fortuitum (13; 7.4%.Comparing the distribution pattern of environmental NTM isolates with clinical isolates suggests a possible transmission link, but this does not apply to all environmental NTM species. Our study confirms an increasing trend of NTM isolation from clinical samples that needs further investigation.

  12. Modelling the molecular composition and nuclear-spin chemistry of collapsing prestellar sources

    Science.gov (United States)

    Hily-Blant, P.; Faure, A.; Rist, C.; Pineau des Forêts, G.; Flower, D. R.

    2018-04-01

    We study the gravitational collapse of prestellar sources and the associated evolution of their chemical composition. We use the University of Grenoble Alpes Astrochemical Network (UGAN), which includes reactions involving the different nuclear-spin states of H2, H+3, and of the hydrides of carbon, nitrogen, oxygen, and sulfur, for reactions involving up to seven protons. In addition, species-to-species rate coefficients are provided for the ortho/para interconversion of the H_3^+ + H2 system and isotopic variants. The composition of the medium is followed from an initial steady state through the early phase of isothermal gravitational collapse. Both the freeze-out of the molecules on to grains and the coagulation of the grains were incorporated in the model. The predicted abundances and column densities of the spin isomers of ammonia and its deuterated forms are compared with those measured recently towards the prestellar cores H-MM1, L16293E, and Barnard B1. We find that gas-phase processes alone account satisfactorily for the observations, without recourse to grain-surface reactions. In particular, our model reproduces both the isotopologue abundance ratios and the ortho:para ratios of NH2D and NHD2 within observational uncertainties. More accurate observations are necessary to distinguish between full scrambling processes—as assumed in our gas-phase network—and direct nucleus- or atom-exchange reactions.

  13. Molecular hydrogen: An abundant energy source for bacterial activity in nuclear waste repositories

    Science.gov (United States)

    Libert, M.; Bildstein, O.; Esnault, L.; Jullien, M.; Sellier, R.

    A thorough understanding of the energy sources used by microbial systems in the deep terrestrial subsurface is essential since the extreme conditions for life in deep biospheres may serve as a model for possible life in a nuclear waste repository. In this respect, H 2 is known as one of the most energetic substrates for deep terrestrial subsurface environments. This hydrogen is produced from abiotic and biotic processes but its concentration in natural systems is usually maintained at very low levels due to hydrogen-consuming bacteria. A significant amount of H 2 gas will be produced within deep nuclear waste repositories, essentially from the corrosion of metallic components. This will consequently improve the conditions for microbial activity in this specific environment. This paper discusses different study cases with experimental results to illustrate the fact that microorganisms are able to use hydrogen for redox processes (reduction of O 2, NO3-, Fe III) in several waste disposal conditions. Consequences of microbial activity include: alteration of groundwater chemistry and shift in geochemical equilibria, gas production or consumption, biocorrosion, and potential modifications of confinement properties. In order to quantify the impact of hydrogen bacteria, the next step will be to determine the kinetic rate of the reactions in realistic conditions.

  14. Molecular hydrogen: An abundant energy source for bacterial activity in nuclear waste repositories

    International Nuclear Information System (INIS)

    Libert, M.; Bildstein, O.; Esnault, L.; Jullien, M.; Sellier, R.

    2011-01-01

    A thorough understanding of the energy sources used by microbial systems in the deep terrestrial subsurface is essential since the extreme conditions for life in deep biospheres may serve as a model for possible life in a nuclear waste repository. In this respect, H 2 is known as one of the most energetic substrates for deep terrestrial subsurface environments. This hydrogen is produced from abiotic and biotic processes but its concentration in natural systems is usually maintained at very low levels due to hydrogen-consuming bacteria. A significant amount of H 2 gas will be produced within deep nuclear waste repositories, essentially from the corrosion of metallic components. This will consequently improve the conditions for microbial activity in this specific environment. This paper discusses different study cases with experimental results to illustrate the fact that microorganisms are able to use hydrogen for redox processes (reduction of O 2 , NO 3- , Fe III) in several waste disposal conditions. Consequences of microbial activity include: alteration of groundwater chemistry and shift in geochemical equilibria, gas production or consumption, bio-corrosion, and potential modifications of confinement properties. In order to quantify the impact of hydrogen bacteria, the next step will be to determine the kinetic rate of the reactions in realistic conditions. (authors)

  15. Automated Source Code Analysis to Identify and Remove Software Security Vulnerabilities: Case Studies on Java Programs

    OpenAIRE

    Natarajan Meghanathan

    2013-01-01

    The high-level contribution of this paper is to illustrate the development of generic solution strategies to remove software security vulnerabilities that could be identified using automated tools for source code analysis on software programs (developed in Java). We use the Source Code Analyzer and Audit Workbench automated tools, developed by HP Fortify Inc., for our testing purposes. We present case studies involving a file writer program embedded with features for password validation, and ...

  16. Wood burning pollution in southern Chile: PM2.5 source apportionment using CMB and molecular markers.

    Science.gov (United States)

    Villalobos, Ana M; Barraza, Francisco; Jorquera, Héctor; Schauer, James J

    2017-06-01

    Temuco is a mid-size city representative of severe wood smoke pollution in southern Chile; i.e., ambient 24-h PM 2.5 concentrations have exceeded 150 μg/m 3 in the winter season and the top concentration reached 372 μg/m 3 in 2010. Annual mean concentrations have decreased but are still above 30 μg/m 3 . For the very first time, a molecular marker source apportionment of ambient organic carbon (OC) and PM 2.5 was conducted in Temuco. Primary resolved sources for PM 2.5 were wood smoke (37.5%), coal combustion (4.4%), diesel vehicles (3.3%), dust (2.2%) and vegetative detritus (0.7%). Secondary inorganic PM 2.5 (sulfates, nitrates and ammonium) contributed 4.8% and unresolved organic aerosols (generated from volatile emissions from incomplete wood combustion), including secondary organic aerosols, contributed 47.1%. Adding the contributions of unresolved organic aerosols to those from primary wood smoke implies that wood burning is responsible for 84.6% of the ambient PM 2.5 in Temuco. This predominance of wood smoke is ultimately due to widespread poverty and a lack of efficient household heating methods. The government has been implementing emission abatement policies but achieving compliance with ambient air quality standards for PM 2.5 in southern Chile remains a challenge. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Molecular DNA identification of blood sources fed on, for Culicine mosquitoes (Diptera: Culicidae collected in the Songkhla province, southern Thailand

    Directory of Open Access Journals (Sweden)

    Theerakamol Pengsakul

    2017-12-01

    Full Text Available Culicine mosquitoes are medically important vectors. Therefore, mosquito control measures are a crucial strategy to interrupt disease transmission. Collection of data on mosquito feeding patterns is crucial for developing an effective vector control strategy. The objective of this study was to use molecular biology methods to identify the sources of DNA in mosquito blood meals. The DNA from blood meals in the mosquito stomachs was extracted and amplified with multiplex PCR, using specific primer sets based on the mitochondrial cytochrome b gene, to identify the DNA sources among human, pig, goat, dog, cow, and chicken. Among the 297 mosquito samples collected in the Songkhla province of Thailand, in Aedes spp. mosquitoes the percentages positive for human, dog, pig, chicken, cow, a mixture of 2 vertebrate DNAs, or of 3, and negative (no identified DNA were 61.90, 2.38, 2.38, 0.60, 0.60, 4.18, 1.20 and 26.79% respectively. In Culex spp. blood meals the rank order was different: fractions positive for chicken, human, dog, cow, goat, pig, a mixture of 2 or 3 vertebrate DNAs, and negative were 40.83, 10.00, 5.00, 4.17, 1.67, 0.83, 8.32, 3.32 and 25.83% respectively. This study shows that feeding behaviors of the two species differ, with most Aedes spp. blood meals containing human blood, while Culex spp. had primarily consumed chicken blood. An improved understanding of the feeding behaviors of mosquitoes could contribute to new, more effective strategies for the control of mosquito populations.

  18. New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0.

    Science.gov (United States)

    Clark, Alex M; Sarker, Malabika; Ekins, Sean

    2014-01-01

    We recently developed a freely available mobile app (TB Mobile) for both iOS and Android platforms that displays Mycobacterium tuberculosis (Mtb) active molecule structures and their targets with links to associated data. The app was developed to make target information available to as large an audience as possible. We now report a major update of the iOS version of the app. This includes enhancements that use an implementation of ECFP_6 fingerprints that we have made open source. Using these fingerprints, the user can propose compounds with possible anti-TB activity, and view the compounds within a cluster landscape. Proposed compounds can also be compared to existing target data, using a näive Bayesian scoring system to rank probable targets. We have curated an additional 60 new compounds and their targets for Mtb and added these to the original set of 745 compounds. We have also curated 20 further compounds (many without targets in TB Mobile) to evaluate this version of the app with 805 compounds and associated targets. TB Mobile can now manage a small collection of compounds that can be imported from external sources, or exported by various means such as email or app-to-app inter-process communication. This means that TB Mobile can be used as a node within a growing ecosystem of mobile apps for cheminformatics. It can also cluster compounds and use internal algorithms to help identify potential targets based on molecular similarity. TB Mobile represents a valuable dataset, data-visualization aid and target prediction tool.

  19. Kinetics of Low Temperature Polyester Dyeing with High Molecular Weight Disperse Dyes by Solvent Microemulsion and AgroSourced Auxiliaries

    Directory of Open Access Journals (Sweden)

    Shahram Radei

    2018-02-01

    Full Text Available This work focused on the evaluation of the kinetics of dyeing polyester fabrics with high molecular weight disperse dyes, at low temperature by solvent microemulsion. This study also compared the effect of two non-toxic agro-sourced auxiliaries (o-vanillin and coumarin using a non-toxic organic solvent. A dyeing bath consisting of a micro-emulsion system involving a small proportion of n-butyl acetate was used, and the kinetics of dyeing were analysed at four temperatures (83, 90, 95 and 100 °C. Moreover, the dyeing rate constants, correlation coefficient and activation energies were proposed for this system. It was found that o-vanillin yielded higher dye absorption levels than coumarin, leading to exhaustions of 88% and 87% for Disperse Red 167 and Disperse Blue 79, respectively. K/S values of dyed polyester were also found to be higher for dye baths containing o-vanillin with respect to the ones with coumarin. In terms of hot pressing fastness and wash fastness, generally no adverse influence on fastness properties was reported, while o-vanillin showed slightly better results compared to coumarin.

  20. Behaviors of beryllium compensation doping in InGaAsP grown by gas source molecular beam epitaxy

    Directory of Open Access Journals (Sweden)

    Y. J. Ma

    2017-07-01

    Full Text Available We report structural properties as well as electrical and optical behaviors of beryllium (Be-doped InGaAsP lattice-matched to InP grown by gas source molecular beam epitaxy. P type layers present a high degree of compensation on the order of 1018 cm−3, and for Be densities below 9.5×1017 cm−3, they are found to be n type. Enhanced incorporation of oxygen during Be doping is observed by secondary ion mass spectroscopy. Be in forms of interstitial donors or donor-like Be-O complexes for cell temperatures below 800°C is proposed to account for such anomalous compensation behaviors. A constant photoluminescence energy of 0.98 eV without any Moss-Burstein shift for Be doping levels up to 1018 cm−3 along with increased emission intensity due to passivation effect of Be is also observed. An increasing number of minority carriers tend to relax via Be defect state-related Shockley-Read-Hall recombination with the increase of Be doping density.

  1. Molecular confirmation of shampoo as the putative source of Pseudomonas aeruginosa-induced postgrooming furunculosis in a dog.

    Science.gov (United States)

    Tham, Heng L; Jacob, Megan E; Bizikova, Petra

    2016-08-01

    An acute onset furunculosis due to Pseudomonas aeruginosa following grooming is a well recognized entity. Although contaminated shampoos have been suspected to be the source of the infection, a molecular confirmation of this association has been missing. This case report describes a dog with postgrooming furunculosis in which Pseudomonas aeruginosa with an identical genetic fingerprint was isolated from the skin lesions as well as from the shampoo used prior to the disease onset. The dog presented for lethargy, anorexia, pain and rapidly progressing skin lesions consistent with haemorrhagic papules, pustules, coalescing ulcers and crusts localized to the dorsal and lateral aspects of the thorax and gluteal region, which developed within 24 h after a bath. Cytology demonstrated suppurative inflammation with occasional intracellular rod-shaped bacteria. Bacterial culture from skin lesions and the shampoo bottle yielded Pseudomonas aeruginosa with an identical pulsed-field gel electrophoresis pattern. Treatment with oral ciprofloxacin and topical antimicrobial shampoo resulted in a complete resolution of skin lesions within eight weeks. Our clinical investigation suggests a link between Pseudomonas-contaminated shampoo and development of postgrooming furunculosis, and underscores the need for hygienic management of shampoos to help limit this disease. © 2016 ESVD and ACVD.

  2. Behaviors of beryllium compensation doping in InGaAsP grown by gas source molecular beam epitaxy

    Science.gov (United States)

    Ma, Y. J.; Zhang, Y. G.; Gu, Y.; Xi, S. P.; Chen, X. Y.; Liang, Baolai; Juang, Bor-Chau; Huffaker, Diana L.; Du, B.; Shao, X. M.; Fang, J. X.

    2017-07-01

    We report structural properties as well as electrical and optical behaviors of beryllium (Be)-doped InGaAsP lattice-matched to InP grown by gas source molecular beam epitaxy. P type layers present a high degree of compensation on the order of 1018 cm-3, and for Be densities below 9.5×1017 cm-3, they are found to be n type. Enhanced incorporation of oxygen during Be doping is observed by secondary ion mass spectroscopy. Be in forms of interstitial donors or donor-like Be-O complexes for cell temperatures below 800°C is proposed to account for such anomalous compensation behaviors. A constant photoluminescence energy of 0.98 eV without any Moss-Burstein shift for Be doping levels up to 1018 cm-3 along with increased emission intensity due to passivation effect of Be is also observed. An increasing number of minority carriers tend to relax via Be defect state-related Shockley-Read-Hall recombination with the increase of Be doping density.

  3. Separation of mouse testis cells on a Celsep (TM) apparatus and their usefulness as a source of high molecular weight DNA or RNA

    Science.gov (United States)

    Wolgemuth, D. J.; Gizang-Ginsberg, E.; Engelmyer, E.; Gavin, B. J.; Ponzetto, C.

    1985-01-01

    The use of a self-contained unit-gravity cell separation apparatus for separation of populations of mouse testicular cells is described. The apparatus, a Celsep (TM), maximizes the unit area over which sedimentation occurs, reduces the amount of separation medium employed, and is quite reproducible. Cells thus isolated have been good sources for isolation of DNA, and notably, high molecular weight RNA.

  4. Herschel observations of extraordinary sources: Analysis of the full Herschel/HIFI molecular line survey of sagittarius B2(N)

    Energy Technology Data Exchange (ETDEWEB)

    Neill, Justin L.; Bergin, Edwin A.; Crockett, Nathan R.; Favre, Cécile; Anderson, Dana E.; Burkhardt, Andrew M.; McNeill, Trevor D. [Department of Astronomy, University of Michigan, 500 Church Street, Ann Arbor, MI 48109 (United States); Lis, Dariusz C.; Emprechtinger, Martin; Monje, Raquel R.; Phillips, Thomas G. [California Institute of Technology, Cahill Center for Astronomy and Astrophysics 301-17, Pasadena, CA 91125 (United States); Schilke, Peter; Comito, Claudia; Qin, Sheng-Li [Physikalisches Institut, Universität zu Köln, Zülpicher Str. 77, D-50937 Köln (Germany); Chen, Jo-Hsin [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109 (United States); Harris, Brent J.; Steber, Amanda L.; Vasyunina, Tatiana [Department of Chemistry, University of Virginia, McCormick Road, Charlottesville, VA 22904 (United States); Lord, Steven D. [National Herschel Science Center, California Institute of Technology, Pasadena, CA 91125 (United States); McGuire, Brett A., E-mail: jneill@umich.edu, E-mail: ebergin@umich.edu [Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 (United States); and others

    2014-07-01

    A sensitive broadband molecular line survey of the Sagittarius B2(N) star-forming region has been obtained with the Heterodyne Instrument for the Far-Infrared (HIFI) instrument on the Herschel Space Observatory, offering the first high spectral resolution look at this well-studied source in a wavelength region largely inaccessible from the ground (625-157 μm). From the roughly 8000 spectral features in the survey, a total of 72 isotopologues arising from 44 different molecules have been identified, ranging from light hydrides to complex organics, and arising from a variety of environments from cold and diffuse to hot and dense gas. We present a local thermodynamic equilibrium (LTE) model to the spectral signatures of each molecule, constraining the source sizes for hot core species with complementary Submillimeter Array interferometric observations and assuming that molecules with related functional group composition are cospatial. For each molecule, a single model is given to fit all of the emission and absorption features of that species across the entire 480-1910 GHz spectral range, accounting for multiple temperature and velocity components when needed to describe the spectrum. As with other HIFI surveys toward massive star-forming regions, methanol is found to contribute more integrated line intensity to the spectrum than any other species. We discuss the molecular abundances derived for the hot core where the LTE approximation is generally found to describe the spectrum well, in comparison to abundances derived for the same molecules in the Orion KL region from a similar HIFI survey. Notably, we find significantly higher abundances of amine- and amide-bearing molecules (CH{sub 3}NH{sub 2}, CH{sub 2}NH, and NH{sub 2}CHO) toward Sgr B2(N) than Orion KL and lower abundances of some complex oxygen-bearing molecules (CH{sub 3}OCHO in particular). In addition to information on the chemical composition of the hot core, the strong far-infrared dust continuum allows

  5. Apportioning sources of organic matter in streambed sediments: An integrated molecular and compound-specific stable isotope approach

    Energy Technology Data Exchange (ETDEWEB)

    Cooper, Richard J., E-mail: Richard.J.Cooper@uea.ac.uk [School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ (United Kingdom); Pedentchouk, Nikolai; Hiscock, Kevin M.; Disdle, Paul [School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ (United Kingdom); Krueger, Tobias [IRI THESys, Humboldt University, 10099 Berlin (Germany); Rawlins, Barry G. [British Geological Survey, Keyworth, Nottingham NG12 5GG (United Kingdom)

    2015-07-01

    We present a novel application for quantitatively apportioning sources of organic matter in streambed sediments via a coupled molecular and compound-specific isotope analysis (CSIA) of long-chain leaf wax n-alkane biomarkers using a Bayesian mixing model. Leaf wax extracts of 13 plant species were collected from across two environments (aquatic and terrestrial) and four plant functional types (trees, herbaceous perennials, and C{sub 3} and C{sub 4} graminoids) from the agricultural River Wensum catchment, UK. Seven isotopic (δ{sup 13}C{sub 27}, δ{sup 13}C{sub 29}, δ{sup 13}C{sub 31}, δ{sup 13}C{sub 27–31}, δ{sup 2}H{sub 27}, δ{sup 2}H{sub 29}, and δ{sup 2}H{sub 27–29}) and two n-alkane ratio (average chain length (ACL), carbon preference index (CPI)) fingerprints were derived, which successfully differentiated 93% of individual plant specimens by plant functional type. The δ{sup 2}H values were the strongest discriminators of plants originating from different functional groups, with trees (δ{sup 2}H{sub 27–29} = − 208‰ to − 164‰) and C{sub 3} graminoids (δ{sup 2}H{sub 27–29} = − 259‰ to − 221‰) providing the largest contrasts. The δ{sup 13}C values provided strong discrimination between C{sub 3} (δ{sup 13}C{sub 27–31} = − 37.5‰ to − 33.8‰) and C{sub 4} (δ{sup 13}C{sub 27–31} = − 23.5‰ to − 23.1‰) plants, but neither δ{sup 13}C nor δ{sup 2}H values could uniquely differentiate aquatic and terrestrial species, emphasizing a stronger plant physiological/biochemical rather than environmental control over isotopic differences. ACL and CPI complemented isotopic discrimination, with significantly longer chain lengths recorded for trees and terrestrial plants compared with herbaceous perennials and aquatic species, respectively. Application of a comprehensive Bayesian mixing model for 18 streambed sediments collected between September 2013 and March 2014 revealed considerable temporal variability in the

  6. The Publicly Available Prebiotic Interstellar Molecular Survey (primos): Expanding Spectroscopic Characterizations, Extending to New Sources, and Adding to the Known Molecular Inventory

    Science.gov (United States)

    McGuire, Brett A.; Carroll, P. Brandon; Corby, Joanna F.; Loomis, Ryan A.; Blake, Geoffrey A.; Hollis, Jan M.; Lovas, Frank J.; Jewell, Philip R.; Remijan, Anthony J.

    2013-06-01

    The publicly available Green Bank Telescope PRebiotic Interstellar MOlecular Survey (PRIMOS) conducted towards Sgr B2(N) provides high resolution, high-sensitivity observations with near-continuous frequency coverage from ˜300 MHz - 50 GHz. Of the eleven new molecular detections in the last year, five (45%) are a direct result of the PRIMOS observations. Further, these observations have recently been used to detect the predicted, but previously unobserved, J = 1-0 and J=2-1 transitions of the newly detected l-C_3H^+ ion. Here, we discuss the analysis of these transitions, as well as recent work to extend the PRIMOS observations to three new regions of interest: VY Canis Majoris, IRC+10216, and NGC 2023. Finally, we highlight the utility of cm-wave surveys in new molecular detections, as well as the value of publicly-available surveys in the approaching era of data-enabled, analysis-limited astrochemistry.

  7. Atmospheric PAHs, NPAHs, and OPAHs at an urban, mountainous, and marine sites in Northern China: Molecular composition, sources, and ageing

    Science.gov (United States)

    Zhang, Junmei; Yang, Lingxiao; Mellouki, Abdelwahid; Chen, Jianmin; Chen, Xiangfeng; Gao, Ying; Jiang, Pan; Li, Yanyan; Yu, Hao; Wang, Wenxing

    2018-01-01

    18 gaseous and particulate polycyclic aromatic hydrocarbons (PAHs), 16 nitro-derivative (NPAHs), and 7 oxy-derivative (OPAHs) were analyzed by Gas Chromatography-Mass Spectrometry (GC-MS) at three locations in Northern China, an urban site (Jinan), a marine site (Tuoji island), and a mountain site (Mt. Tai). The combined gas and particulate concentrations of 18 PAHs, 16 NPAHs, and 7 OPAHs were highest at the urban site (305.91, 2.80, and 9.05 ng/m3, respectively) and lowest at the mountain location (37.83, 0.27, and 1.59 ng/m3, respectively). A noticeable increase in the high molecular weight PAHs was observed during polluted conditions compared to clean conditions. Diagnostic ratios clearly demonstrated that coal/biomass combustion was the major PAH source in Northern China. The particulate PAHs were the most aged at the mountain site due to long-distance atmospheric transport. The formation rate of NPAHs was most efficient at the mountain location and during heavily polluted days at the urban and marine sites. In addition, the main formation pathway for NPAHs was through the OH initiated secondary reaction. NO3 radicals most significantly contributed to the NPAHs formation at night, during clear weather, and at the mountain site. The logKp value was lowest at the urban site for most individual compounds and highest at the mountain site. Higher logKp was found for NPAHs and OPAHs compared with their corresponding parent PAHs. The linear regression of logKp vs logPL0 at the three sites suggested that the gas-particle partitioning of PAHs might be in non-equilibrium.

  8. Using non-invasive molecular spectroscopic techniques to detect unique aspects of protein Amide functional groups and chemical properties of modeled forage from different sourced-origins.

    Science.gov (United States)

    Ji, Cuiying; Zhang, Xuewei; Yu, Peiqiang

    2016-03-05

    The non-invasive molecular spectroscopic technique-FT/IR is capable to detect the molecular structure spectral features that are associated with biological, nutritional and biodegradation functions. However, to date, few researches have been conducted to use these non-invasive molecular spectroscopic techniques to study forage internal protein structures associated with biodegradation and biological functions. The objectives of this study were to detect unique aspects and association of protein Amide functional groups in terms of protein Amide I and II spectral profiles and chemical properties in the alfalfa forage (Medicago sativa L.) from different sourced-origins. In this study, alfalfa hay with two different origins was used as modeled forage for molecular structure and chemical property study. In each forage origin, five to seven sources were analyzed. The molecular spectral profiles were determined using FT/IR non-invasive molecular spectroscopy. The parameters of protein spectral profiles included functional groups of Amide I, Amide II and Amide I to II ratio. The results show that the modeled forage Amide I and Amide II were centered at 1653 cm(-1) and 1545 cm(-1), respectively. The Amide I spectral height and area intensities were from 0.02 to 0.03 and 2.67 to 3.36 AI, respectively. The Amide II spectral height and area intensities were from 0.01 to 0.02 and 0.71 to 0.93 AI, respectively. The Amide I to II spectral peak height and area ratios were from 1.86 to 1.88 and 3.68 to 3.79, respectively. Our results show that the non-invasive molecular spectroscopic techniques are capable to detect forage internal protein structure features which are associated with forage chemical properties. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Molecular beam epitaxy growth of niobium oxides by solid/liquid state oxygen source and lithium assisted metal-halide chemistry

    Science.gov (United States)

    Tellekamp, M. Brooks; Greenlee, Jordan D.; Shank, Joshua C.; Doolittle, W. Alan

    2015-09-01

    In order to consistently grow high quality niobium oxides and lithium niobium oxides, a novel solid/liquid state oxygen source, LiClO4, has been implemented in a molecular beam epitaxy (MBE) system. LiClO4 is shown to decompose into both molecular and atomic oxygen upon heating. This allows oxidation rates similar to that of molecular oxygen but at a reduced overall beam flux, quantified by in situ Auger analysis. LiClO4 operation is decomposition limited to less than 400 °C, and other material limitations are identified. The design of a custom near-ambient NbCl5 effusion cell is presented, which improves both short and long term stability. Films of Nb oxidation state +2, +3, and +5 are grown using these new tools, including the multi-functional sub-oxide LiNbO2.

  10. Si(001):B gas-source molecular-beam epitaxy: Boron surface segregation and its effect on film growth kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Kim, H.; Glass, G.; Spila, T.; Taylor, N.; Park, S.Y.; Abelson, J.R.; Greene, J.E. [Department of Materials Science, Coordinated Science Laboratory, and Materials Research Laboratory, University of Illinois, 1101 West Springfield, Urbana, Illinois 61801 (United States)

    1997-09-01

    B-doped Si(001) films, with concentrations C{sub B} up to 1.7{times}10{sup 22}cm{sup {minus}3}, were grown by gas-source molecular-beam epitaxy from Si{sub 2}H{sub 6} and B{sub 2}H{sub 6} at T{sub s}=500{endash}800{degree}C. D{sub 2} temperature-programed desorption (TPD) spectra were then used to determine B coverages {theta}{sub B} as a function of C{sub B} and T{sub s}. In these measurements, as-deposited films were flash heated to desorb surface hydrogen, cooled, and exposed to atomic deuterium until saturation coverage. Strong B surface segregation was observed with surface-to-bulk B concentration ratios ranging up to 1200. TPD spectra exhibited {beta}{sub 2} and {beta}{sub 1} peaks associated with dideuteride and monodeuteride desorption as well as lower-temperature B-induced peaks {beta}{sub 2}{sup {asterisk}} and {beta}{sub 1}{sup {asterisk}}. Increasing {theta}{sub B} increased the area under {beta}{sub 2}{sup {asterisk}} and {beta}{sub 1}{sup {asterisk}} at the expense of {beta}{sub 2} and {beta}{sub 1} and decreased the total D coverage {theta}{sub D}. The TPD results were used to determine the B segregation enthalpy, {minus}0.53eV, and to explain and model the effects of high B coverages on Si(001) growth kinetics. Film deposition rates R increase by {ge}50{percent} with increasing C{sub B}{tilde {gt}}1{times}10{sup 19}cm{sup {minus}3} at T{sub s}{le}550{degree}C, due primarily to increased H desorption rates from B-backbonded Si adatoms, and decrease by corresponding amounts at T{sub s}{ge}600{degree}C due to decreased adsorption site densities. At T{sub s}{ge}700{degree}C, high B coverages also induce {l_brace}113{r_brace} facetting. {copyright} {ital 1997 American Institute of Physics.}

  11. Parametrics for Molecular Deuterium Concentrations in the Source Region of the UW-IEC Device Using an Ion Acoustic Wave Diagnostic

    Science.gov (United States)

    Boris, D. R.; Emmert, G. A.

    2007-11-01

    The ion source region of the UW-Inertial Electrostatic Confinement device is comprised of a filament assisted DC discharge plasma that exists between the wall of the IEC vacuum chamber and the grounded spherical steel grid that makes up the anode of the IEC device. A 0-dimensional rate equation calculation of the molecular deuterium ion species concentration has been applied utilizing varying primary electron energy, and neutral gas pressure. By propagating ion acoustic waves in the source region of the IEC device the concentrations of molecular deuterium ion species have been determined for these varying plasma conditions, and high D3^+ concentrations have been verified. This was done by utilizing the multi-species ion acoustic wave dispersion relation, which relates the phase speed of the multi-species ion acoustic wave, vph, to the sum in quadrature of the concentration weighted ion acoustic sound speeds of the individual ion species.

  12. Characterizing and sourcing ambient PM2.5 over key emission regions in China II: Organic molecular markers and CMB modeling

    Science.gov (United States)

    Zhou, Jiabin; Xiong, Ying; Xing, Zhenyu; Deng, Junjun; Du, Ke

    2017-08-01

    From November 2012 to July 2013, a sampling campaign was completed for comprehensive characterization of PM2.5 over four key emission regions in China: Beijing-Tianjin-Hebei (BTH), Yangzi River Delta (YRD), Pearl River Delta (PRD), and Sichuan Basin (SB). A multi-method approach, adopting different analytical and receptor modeling methods, was employed to determine the relative abundances of region-specific air pollution constituents and contributions of emission sources. This paper is focused on organic molecular marker based source apportionment using chemical mass balance (CMB) receptor modeling. Analyses of the organic molecular markers revealed that vehicle emission, coal combustion, biomass burning, meat cooking and natural gas combustion were the major contributors to organic carbon (OC) in PM2.5. The vehicle emission dominated the sources contributing to OC in spring at four sampling sites. During wintertime, the coal combustion had highest contribution to OC at BTH site, while the major source contributing to OC at YRD and PRD sites was vehicle emission. In addition, the relative contributions of different emission sources to PM2.5 mass at a specific location site and in a specific season revealed seasonal and spatial variations across all four sampling locations. The largest contributor to PM2.5 mass was secondary sulfate (14-17%) in winter at the four sites. The vehicle emission was found to be the major source (14-21%) for PM2.5 mass at PRD site. The secondary ammonium has minor variation (4-5%) across the sites, confirming the influences of regional emission sources on these sites. The distinct patterns of seasonal and spatial variations of source apportionment observed in this study were consistent with the findings in our previous paper based upon water-soluble ions and carbonaceous fractions. This makes it essential for the local government to make season- and region-specific mitigation strategies for abating PM2.5 pollution in China.

  13. System for Informatics in the Molecular Pathology Laboratory: An Open-Source End-to-End Solution for Next-Generation Sequencing Clinical Data Management.

    Science.gov (United States)

    Kang, Wenjun; Kadri, Sabah; Puranik, Rutika; Wurst, Michelle N; Patil, Sushant A; Mujacic, Ibro; Benhamed, Sonia; Niu, Nifang; Zhen, Chao Jie; Ameti, Bekim; Long, Bradley C; Galbo, Filipo; Montes, David; Iracheta, Crystal; Gamboa, Venessa L; Lopez, Daisy; Yourshaw, Michael; Lawrence, Carolyn A; Aisner, Dara L; Fitzpatrick, Carrie; McNerney, Megan E; Wang, Y Lynn; Andrade, Jorge; Volchenboum, Samuel L; Furtado, Larissa V; Ritterhouse, Lauren L; Segal, Jeremy P

    2018-04-24

    Next-generation sequencing (NGS) diagnostic assays increasingly are becoming the standard of care in oncology practice. As the scale of an NGS laboratory grows, management of these assays requires organizing large amounts of information, including patient data, laboratory processes, genomic data, as well as variant interpretation and reporting. Although several Laboratory Information Systems and/or Laboratory Information Management Systems are commercially available, they may not meet all of the needs of a given laboratory, in addition to being frequently cost-prohibitive. Herein, we present the System for Informatics in the Molecular Pathology Laboratory, a free and open-source Laboratory Information System/Laboratory Information Management System for academic and nonprofit molecular pathology NGS laboratories, developed at the Genomic and Molecular Pathology Division at the University of Chicago Medicine. The System for Informatics in the Molecular Pathology Laboratory was designed as a modular end-to-end information system to handle all stages of the NGS laboratory workload from test order to reporting. We describe the features of the system, its clinical validation at the Genomic and Molecular Pathology Division at the University of Chicago Medicine, and its installation and testing within a different academic center laboratory (University of Colorado), and we propose a platform for future community co-development and interlaboratory data sharing. Copyright © 2018. Published by Elsevier Inc.

  14. Investigation of natural phosphatidylcholine sources: separation and identification by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS2) of molecular species.

    Science.gov (United States)

    Le Grandois, Julie; Marchioni, Eric; Zhao, Minjie; Giuffrida, Francesca; Ennahar, Saïd; Bindler, Françoise

    2009-07-22

    This study is a contribution to the exploration of natural phospholipid (PL) sources rich in long-chain polyunsaturated fatty acids (LC-PUFAs) with nutritional interest. Phosphatidylcholines (PCs) were purified from total lipid extracts of different food matrices, and their molecular species were separated and identified by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS(2)). Fragmentation of lithiated adducts allowed for the identification of fatty acids linked to the glycerol backbone. Soy PC was particularly rich in species containing essential fatty acids, such as (18:2-18:2)PC (34.0%), (16:0-18:2)PC (20.8%), and (18:1-18:2)PC (16.3%). PC from animal sources (ox liver and egg yolk) contained major molecular species, such as (16:0-18:2)PC, (16:0-18:1)PC, (18:0-18:2)PC, or (18:0-18:1)PC. Finally, marine source (krill oil), which was particularly rich in (16:0-20:5)PC and (16:0-22:6)PC, appeared to be an interesting potential source for food supplementation with LC-PUFA-PLs, particularly eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA).

  15. Ge(001):B gas-source molecular beam epitaxy: B surface segregation, hydrogen desorption, and film growth kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Kim, H.; Greene, J.E. [Materials Science Department, the Coordinated Science Laboratory and the Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801 (United States)

    1999-03-01

    Ultrahigh B-doped Ge(001) layers, with concentrations C{sub B} up to 8{times}10{sup 21} cm{sup {minus}3}, were grown by gas-source molecular beam epitaxy from Ge{sub 2}H{sub 6} and B{sub 2}H{sub 6} at temperatures T{sub s}=325{degree}C (in the surface-reaction-limited regime) and 600{degree}C (in the flux-limited regime). The samples were quenched, D site exchanged for H, and D{sub 2} temperature-programed desorption (TPD) used to determine B coverages {theta}{sub B} as a function of C{sub B} and T{sub s} by comparison with B-adsorbed Ge(001) reference samples with known {theta}{sub B} values. During Ge(001):B film growth, strong surface B segregation to the second layer was observed with surface-to-bulk B concentration ratios ranging up to 6000. The TPD spectra exhibited {alpha}{sub 2} and {alpha}{sub 1} peaks associated with dideuteride and monodeuteride desorption as well as lower-temperature B-induced {alpha}{sub 2}{sup {asterisk}} and {alpha}{sub 1}{sup {asterisk}} peaks associated with deuterium desorption from Ge{sup {asterisk}} surface atoms with B backbonds. Increasing {theta}{sub B} expanded the area under {alpha}{sub 2}{sup {asterisk}} and {alpha}{sub 1}{sup {asterisk}} at the expense of {alpha}{sub 2} and {alpha}{sub 1} and decreased the total D coverage {theta}{sub D}. The TPD results were used to determine the B segregation enthalpy, {minus}0.64 eV, and to explain and model the effects of high B coverages on Ge(001) growth kinetics. At T{sub s}=325{degree}C, where B segregation is kinetically hindered, film deposition rates R{sub Ge} are not a strong function of C{sub B}, exhibiting only a small decrease at C{sub B}{approx_gt}5{times}10{sup 18} cm{sup {minus}3}. However, at T{sub s}=600{degree}C, R{sub Ge} decreases by up to 40{percent} with increasing C{sub B}{approx_gt}1{times}10{sup 18} cm{sup {minus}3}. This is due primarily to the combination of B-induced Ge dimer vacancies and the deactivation of surface dangling bonds caused by charge transfer

  16. Thorium molecular negative ion production in a cesium sputter source at BARC-TIFR pelletron accelerator ion source test set up

    International Nuclear Information System (INIS)

    Gupta, A.K.; Mehrotra, N.; Kale, R.M.; Alamelu, D.; Aggarwal, S.K.

    2005-01-01

    Ion source test set up at Pelletron Accelerator facility has been utilized extensively for the production and characterization of negative ions, with particular emphasis being place at the species of experimental users interest. The attention have been focussed towards the formation of rare earth negative ions, due to their importance in the ongoing accelerator mass spectroscopy program and isotopic abundance measurements using secondary negative ion mass spectrometry

  17. Submicron particulate organic matter in the urban atmosphere: a new method for real-time measurement, molecular-level characterization and source apportionment

    Science.gov (United States)

    Müller, Markus; Eichler, Philipp; D'Anna, Barbara; Tan, Wen; Wisthaler, Armin

    2017-04-01

    We used a novel chemical analytical method for measuring submicron particulate organic matter in the atmosphere of three European cities (Innsbruck, Lyon, Valencia). Proton-Transfer-Reaction Time-of-Flight Mass Spectrometry (PTR-ToF-MS) was used in combination with the "chemical analysis of aerosol online" (CHARON) inlet for detecting particulate organic compounds on-line (i.e. without filter pre-collection), in real-time (1-min time resolution), at ng m-3 concentrations, with molecular-level resolution (i.e. obtaining molecular weight and elemental composition information). The CHARON-PTR-ToF-MS system monitored molecular tracers associated with different particle sources including levoglucosan from biomass combustion, PAHs from vehicular traffic, nicotine from cigarette smoking, and monoterpene oxidation products secondarily formed from biogenic emissions. The tracer information was used for interpreting positive matrix factorization (PMF) data which allowed us to apportion the sources of submicron particulate organic matter in the different urban environments. This work was funded through the PIMMS ITN, which was supported by the European Commission's 7th Framework Programme under grant agreement number 287382.

  18. Molecular structure of sodium lignosulfonate from different sources and their properties as dispersant of TiO2 slurry

    Science.gov (United States)

    Haifeng Zhou; Dongjie Yang; Junyong Zhu

    2016-01-01

    The molecular structure and properties of four sodium lignosulfates (LSs) derived from pulping or bioethanol production were evaluated and compared. SXP and SAL were produced by sulfite pulping and sulfonation reaction of lignin from alkali pulping of poplar, respectively. LS-180 and LS-150 were from sulfite pretreatment to overcome recalcitrance of lignocelluloses (...

  19. MOLECULAR CHARACTERIZATION OF MICROSPORIDIA INDICATES THAT FUR-BEARING WILD MAMMALS CAN BE A SOURCE OF HUMAN PATHOGENIC ENTEROCYTOZOON BIENEUSI

    Science.gov (United States)

    Over 13 months, 465 beavers, foxes, muskrats, otters, and raccoons were trapped in four counties in eastern Maryland and examined by molecular methods for microsporidia. A two-step nested PCR protocol was developed to amplify a 392 bp fragment of the internal transcribed spacer (...

  20. Formation of atomic clusters through the laser ablation of refractory materials in a supersonic molecular beam source

    International Nuclear Information System (INIS)

    Haufler, R.E.; Puretzky, A.A.; Compton, R.N.

    1993-01-01

    Concepts which guide the design of atomic cluster supersonic beam sources have been developed. These ideas are founded on the knowledge of laser ablation dynamics and are structured in order to take advantage of certain features of the ablation event. Some of the drawbacks of previous cluster source designs become apparent when the sequence of events following laser ablation are clarified. Key features of the new cluster source design include control of the cluster size distribution, uniform performance with a variety of solid materials and elements, high beam intensity, and significant removal of internal energy during the supersonic expansion

  1. Application of leftover sample material from waterborne protozoa monitoring for the molecular detection of Bacteroidales and fecal source tracking markers

    Science.gov (United States)

    In this study, we examined the potential for detecting fecal bacteria and microbial source tracking markers in samples discarded during the concentration of Cryptosporidium and Giardia using USEPA Method 1623. Recovery rates for different fecal bacteria were determined using sp...

  2. The Molecular Level Characterization of Biodegradable Polymers Originated from Polyethylene Using Non-Oxygenated Polyethylene Wax as a Carbon Source for Polyhydroxyalkanoate Production.

    Science.gov (United States)

    Johnston, Brian; Jiang, Guozhan; Hill, David; Adamus, Grazyna; Kwiecień, Iwona; Zięba, Magdalena; Sikorska, Wanda; Green, Matthew; Kowalczuk, Marek; Radecka, Iza

    2017-08-28

    There is an increasing demand for bio-based polymers that are developed from recycled materials. The production of biodegradable polymers can include bio-technological (utilizing microorganisms or enzymes) or chemical synthesis procedures. This report demonstrates the corroboration of the molecular structure of polyhydroxyalkanoates (PHAs) obtained by the conversion of waste polyethylene (PE) via non-oxygenated PE wax (N-PEW) as an additional carbon source for a bacterial species. The N-PEW, obtained from a PE pyrolysis reaction, has been found to be a beneficial carbon source for PHA production with Cupriavidus necator H16. The production of the N-PEW is an alternative to oxidized polyethylene wax (O-PEW) (that has been used as a carbon source previously) as it is less time consuming to manufacture and offers fewer industrial applications. A range of molecular structural analytical techniques were performed on the PHAs obtained; which included nuclear magnetic resonance (NMR) and electrospray ionisation tandem mass spectrometry (ESI-MS/MS). Our study showed that the PHA formed from N-PEW contained 3-hydroxybutyrate (HB) with 11 mol% of 3-hydroxyvalerate (HV) units.

  3. Molecular Chemical Structure of Barley Proteins Revealed by Ultra-Spatially Resolved Synchrotron Light Sourced FTIR Microspectroscopy: Comparison of Barley Varieties

    International Nuclear Information System (INIS)

    Yu, P.

    2007-01-01

    Barley protein structure affects the barley quality, fermentation, and degradation behavior in both humans and animals among other factors such as protein matrix. Publications show various biological differences among barley varieties such as Valier and Harrington, which have significantly different degradation behaviors. The objectives of this study were to reveal the molecular structure of barley protein, comparing various varieties (Dolly, Valier, Harrington, LP955, AC Metcalfe, and Sisler), and quantify protein structure profiles using Gaussian and Lorentzian methods of multi-component peak modeling by using the ultra-spatially resolved synchrotron light sourced Fourier transform infrared microspectroscopy (SFTIRM). The items of the protein molecular structure revealed included protein structure α-helices, β-sheets, and others such as β-turns and random coils. The experiment was performed at the National Synchrotron Light Source in Brookhaven National Laboratory (BNL, US Department of Energy, NY). The results showed that with the SFTIRM, the molecular structure of barley protein could be revealed. Barley protein structures exhibited significant differences among the varieties in terms of proportion and ratio of model-fitted α-helices, β-sheets, and others. By using multi-component peaks modeling at protein amide I region of 1710-1576 cm -1 , the results show that barley protein consisted of approximately 18-34% of α-helices, 14-25% of β-sheets, and 44-69% others. AC Metcalfe, Sisler, and LP955 consisted of higher (P 0.05). The ratio of α-helices to others (0.3 to 1.0, P < 0.05) and that of β-sheets to others (0.2 to 0.8, P < 0.05) were different among the barley varieties. It needs to be pointed out that using a multi-peak modeling for protein structure analysis is only for making relative estimates and not exact determinations and only for the comparison purpose between varieties. The principal component analysis showed that protein amide I Fourier

  4. Determination of sulfur in bovine serum albumin and L-cysteine using high-resolution continuum source molecular absorption spectrometry of the CS molecule

    Science.gov (United States)

    Andrade-Carpente, Eva; Peña-Vázquez, Elena; Bermejo-Barrera, Pilar

    2016-08-01

    In this study, the content of sulfur in bovine serum albumin and L-cysteine was determined using high-resolution continuum source molecular absorption spectrometry of the CS molecule, generated in a reducing air-acetylene flame. Flame conditions (height above the burner, measurement time) were optimized using a 3.0% (v/v) sulfuric acid solution. A microwave lab station (Ethos Plus MW) was used for the digestion of both compounds. During the digestion step, sulfur was converted to sulfate previous to the determination. Good repeatability (4-10%) and analytical recovery (91-106%) was obtained.

  5. InAs/GaAs quantum dot lasers with InGaP cladding layer grown by solid-source molecular-beam epitaxy

    International Nuclear Information System (INIS)

    Yeh, N.-T.; Liu, W.-S.; Chen, S.-H.; Chiu, P.-C.; Chyi, J.-I.

    2002-01-01

    This letter presents the lasing properties of InAs/GaAs quantum dot lasers with InGaP cladding layers grown by solid-source molecular-beam epitaxy. These Al-free lasers exhibit a threshold current density of 138 A/cm 2 , an internal loss of 1.35 cm -1 , and an internal quantum efficiency of 31% at room temperature. At a low temperature, a very high characteristic temperature of 425 K and very low threshold current density of 30 A/cm 2 are measured

  6. Versatile user-oriented atomic and molecular beam apparatus for use with the National Synchrotron Light Source

    International Nuclear Information System (INIS)

    Mitchell, J.B.A.; Grover, J.R.

    1978-11-01

    A proposed atomic and moleuclar beam apparatus is described for photon interaction studies using the National Sychrotron Light Source at the Brookhaven National Laboratory. This apparatus will employ ultrahigh vacuum techniques compatible with storage ring operation. Supersonic nozzle sources will be used to produce the beams and signal detection will be accomplished using a quadrupole mass analysis system. The equipment is intended for use both by in-house and outside users and primary consideration has been given to flexibility of design. The application of photoionization techniques to the study of crossed beam reactive scattering with particular emphasis on internal energy distribution analysis is discussed

  7. Relationship between THMs/NDMA formation potential and molecular weight of organic compounds for source and treated water in Shanghai, China.

    Science.gov (United States)

    An, Dong; Gu, Bin; Sun, Sainan; Zhang, Han; Chen, Yanan; Zhu, Huifeng; Shi, Jian; Tong, Jun

    2017-12-15

    Molecular weight (MW) distributions in source and treated water in Shanghai, China were investigated to understand the relationship between trihalomethanes formation potential/N-nitrosodimethylamine formation potential (THMFP/NDMAFP) and dissolved organic carbon (DOC) for different MW ranges (30KDa). The result of MW distributions in source water indicated a relationship between THMFP/NDMAFP and DOC such that DOC for 30KDa THMFP was totally removed whereas NDMA according to the results for treated water between DOC and NDMAFP (R 2 =0.94 and 0.93 for sand and GAC filtration, respectively). The results may provide researchers with targeted treatment strategies to destroy, remove, or reduce the occurrence of THMs and NDMA precursors. The findings presented in this study will be of great value in future work for selecting suitable drinking water treatment processes to minimize the formation of disinfection by-products using chlorine or chloramine disinfection. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Molecular isotopic characterisation of hydrocarbon biomarkers in Palaeocene-Eocene evaporitic, lacustrine source rocks from the Jianghan Basin, China

    NARCIS (Netherlands)

    Sinninghe Damsté, J.S.; Grice, Kliti; Schouten, S.; Peters, Kenneth E.

    1998-01-01

    Immature organic matter in lacustrine source rocks from the Jianghan Basin, eastern China, was studied for distributions and stable carbon isotopic compositions (13C) of hydrocarbon biomarkers. All of the bitumens contain isorenieratane (13C ca. −17 ) indicating the presence of Chlorobiaceae, and

  9. Determination of phospholipids in soybean lecithin samples via the phosphorus monoxide molecule by high-resolution continuum source graphite furnace molecular absorption spectrometry.

    Science.gov (United States)

    Pires, Laís N; Brandão, Geovani C; Teixeira, Leonardo S G

    2017-06-15

    This paper presents a method for determining phospholipids in soybean lecithin samples by phosphorus determination using high-resolution continuum source graphite furnace molecular absorption spectrometry (HR-CS GF MAS) via molecular absorption of phosphorus monoxide. Samples were diluted in methyl isobutyl ketone. The best conditions were found to be 213.561nm with a pyrolysis temperature of 1300°C, a volatilization temperature of 2300°C and Mg as a chemical modifier. To increase the analytical sensitivity, measurement of the absorbance signal was obtained by summing molecular transition lines for PO surrounding 213nm: 213.561, 213.526, 213.617 and 213.637nm. The limit of detection was 2.35mgg -1 and the precision, evaluated as relative standard deviation (RSD), was 2.47% (n=10) for a sample containing 2.2% (w/v) phosphorus. The developed method was applied for the analysis of commercial samples of soybean lecithin. The determined concentrations of phospholipids in the samples varied between 38.1 and 45% (w/v). Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. CaI and SrI molecules for iodine determination by high-resolution continuum source graphite furnace molecular absorption spectrometry: Greener molecules for practical application.

    Science.gov (United States)

    Zanatta, Melina Borges Teixeira; Nakadi, Flávio Venâncio; da Veiga, Márcia Andreia Mesquita Silva

    2018-03-01

    A new method to determine iodine in drug samples by high-resolution continuum source graphite furnace molecular absorption spectrometry (HR-CS GF MAS) has been developed. The method measures the molecular absorption of a diatomic molecule, CaI or SrI (less toxic molecule-forming reagents), at 638.904 or 677.692nm, respectively, and uses a mixture containing 5μg of Pd and 0.5μg of Mg as chemical modifier. The method employs pyrolysis temperatures of 1000 and 800°C and vaporization temperatures of 2300 and 2400°C for CaI and SrI, respectively. The optimized amounts of Ca and Sr as molecule-forming reagents are 100 and 150µg, respectively. On the basis of interference studies, even small chlorine concentrations reduce CaI and SrI absorbance significantly. The developed method was used to analyze different commercial drug samples, namely thyroid hormone pills with three different iodine amounts (15.88, 31.77, and 47.66µg) and one liquid drug with 1% m v -1 active iodine in their compositions. The results agreed with the values informed by the manufacturers (95% confidence level) regardless of whether CaI or SrI was determined. Therefore, the developed method is useful for iodine determination on the basis of CaI or SrI molecular absorption. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Molecular mechanisms behind the adjustment of phototrophic light-harvesting and mixotrophic utilization of cellulosic carbon sources in Chlamydomonas reinhardtii

    OpenAIRE

    Blifernez-Klassen, Olga

    2012-01-01

    Plants, green algae and cyanobacteria perform photosynthetic conversion of sunlight into chemical energy in a permanently changing natural environment, where the efficient utilization of light and inorganic carbon represent the most critical factors. Photosynthetic organisms have developed different acclimation strategies to adapt changing light conditions and insufficient carbon source supply in order to survive and to assure optimal growth and protection. This thesis provides further insigh...

  12. Carbon sources in suspended particles and surface sediments from the Beaufort Sea revealed by molecular lipid biomarkers and compound-specific isotope analysis

    Directory of Open Access Journals (Sweden)

    I. Tolosa

    2013-03-01

    Full Text Available Molecular lipid biomarkers (hydrocarbons, alcohols, sterols and fatty acids and compound-specific isotope analysis of suspended particulate organic matter (SPM and surface sediments of the Mackenzie Shelf and slope (southeast Beaufort Sea, Arctic Ocean were studied in summer 2009. The concentrations of the molecular lipid markers, characteristic of known organic matter sources, were grouped and used as proxies to evaluate the relative importance of fresh algal, detrital algal, fossil, C3 terrestrial plants, bacterial and zooplankton material in the organic matter (OM of this area. Fossil and detrital algal contributions were the major fractions of the freshwater SPM from the Mackenzie River with ~34% each of the total molecular biomarkers. Fresh algal, C3 terrestrial, bacterial and zooplanktonic components represented much lower percentages, 17, 10, 4 and 80%, with a minor contribution of fossil and C3 terrestrial biomarkers. Characterization of the sediments revealed a major sink of refractory algal material mixed with some fresh algal material, fossil hydrocarbons and a small input of C3 terrestrial sources. In particular, the sediments from the shelf and at the mouth of the Amundsen Gulf presented the highest contribution of detrital algal material (60–75%, whereas those from the slope contained the highest proportion of fossil (40% and C3 terrestrial plant material (10%. Overall, considering that the detrital algal material is marine derived, autochthonous sources contributed more than allochthonous sources to the OM lipid pool. Using the ratio of an allochthonous biomarker (normalized to total organic carbon, TOC found in the sediments to those measured at the river mouth water, we estimated that the fraction of terrestrial material preserved in the sediments accounted for 30–40% of the total carbon in the inner shelf sediments, 17% in the outer shelf and Amundsen Gulf and up to 25% in the slope sediments. These estimates are low

  13. SU-G-IeP3-10: Molecular Imaging with Clinical X-Ray Sources and Compton Cameras

    International Nuclear Information System (INIS)

    Vernekohl, D; Ahmad, M; Chinn, G; Xing, L

    2016-01-01

    Purpose: The application of Compton cameras (CC) is a novel approach translating XFCT to a practical modality realized with clinical CT systems without the restriction of pencil beams. The dual modality design offers additional information without extra patient dose. The purpose of this work is to investigate the feasibility and efficacy of using CCs for volumetric x-ray fluorescence (XF) imaging by Monte Carlo (MC) simulations and statistical image reconstruction. Methods: The feasibility of a CC for imaging x-ray fluorescence emitted from targeted lesions is examined by MC simulations. 3 mm diameter water spheres with various gold concentrations and detector distances are placed inside the lung of an adult human phantom (MIRD) and are irradiated with both fan and cone-beam geometries. A sandwich design CC composed of Silicon and CdTe is used to image the gold nanoparticle distribution. The detection system comprises four 16×26 cm"2 detector panels placed on the chest of a MIRD phantom. Constraints of energy-, spatial-resolution, clinical geometries and Doppler broadening are taken into account. Image reconstruction is performed with a list-mode MLEM algorithm with cone-projector on a GPU. Results: The comparison of reconstruction of cone- and fan-beam excitation shows that the spatial resolution is improved by 23% for fan-beams with significantly decreased processing time. Cone-beam excitation increases scatter content disturbing quantification of lesions near the body surface. Spatial resolution and detectability limit in the center of the lung is 8.7 mm and 20 fM for 50 nm diameter gold nanoparticles at 20 mGy. Conclusion: The implementation of XFCT with a CC is a feasible method for molecular imaging with high atomic number probes. Given constrains of detector resolutions, Doppler broadening, and limited exposure dose, spatial resolutions comparable with PET and molecular sensitivities in the fM range are realizable with current detector technology.

  14. SU-G-IeP3-10: Molecular Imaging with Clinical X-Ray Sources and Compton Cameras

    Energy Technology Data Exchange (ETDEWEB)

    Vernekohl, D; Ahmad, M; Chinn, G; Xing, L [Stanford University, Stanford, CA (United States)

    2016-06-15

    Purpose: The application of Compton cameras (CC) is a novel approach translating XFCT to a practical modality realized with clinical CT systems without the restriction of pencil beams. The dual modality design offers additional information without extra patient dose. The purpose of this work is to investigate the feasibility and efficacy of using CCs for volumetric x-ray fluorescence (XF) imaging by Monte Carlo (MC) simulations and statistical image reconstruction. Methods: The feasibility of a CC for imaging x-ray fluorescence emitted from targeted lesions is examined by MC simulations. 3 mm diameter water spheres with various gold concentrations and detector distances are placed inside the lung of an adult human phantom (MIRD) and are irradiated with both fan and cone-beam geometries. A sandwich design CC composed of Silicon and CdTe is used to image the gold nanoparticle distribution. The detection system comprises four 16×26 cm{sup 2} detector panels placed on the chest of a MIRD phantom. Constraints of energy-, spatial-resolution, clinical geometries and Doppler broadening are taken into account. Image reconstruction is performed with a list-mode MLEM algorithm with cone-projector on a GPU. Results: The comparison of reconstruction of cone- and fan-beam excitation shows that the spatial resolution is improved by 23% for fan-beams with significantly decreased processing time. Cone-beam excitation increases scatter content disturbing quantification of lesions near the body surface. Spatial resolution and detectability limit in the center of the lung is 8.7 mm and 20 fM for 50 nm diameter gold nanoparticles at 20 mGy. Conclusion: The implementation of XFCT with a CC is a feasible method for molecular imaging with high atomic number probes. Given constrains of detector resolutions, Doppler broadening, and limited exposure dose, spatial resolutions comparable with PET and molecular sensitivities in the fM range are realizable with current detector technology.

  15. Development of novel HER2 inhibitors against gastric cancer derived from flavonoid source of Syzygium alternifolium through molecular dynamics and pharmacophore-based screening

    Directory of Open Access Journals (Sweden)

    Babu TMC

    2016-11-01

    Full Text Available Tirumalasetty Muni Chandra Babu,1 Aluru Rammohan,2 Vijaya Bhaskar Baki,1 Savita Devi,3 Duvvuru Gunasekar,2 Wudayagiri Rajendra1 1Bioinformatics Center, Division of Molecular Biology, Department of Zoology, 2Natural Products Division, Department of Chemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, 3Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India Abstract: Continuous usage of synthetic chemotherapeutic drugs causes adverse effects, which prompted for the development of alternative therapeutics for gastric cancer from natural source. This study was carried out with a specific aim to screen gastroprotective compounds from the fruits of Syzygium alternifolium (Myrtaceae. Three flavonoids, namely, 1 5-hydroxy-7,4'-dimethoxy-6,8-di-C-methylflavone, 2 kaempferol-3-O-β-D-glucopyranoside, and 3 kaempferol-3-O-α-L-rhamnopyranoside were isolated from the above medicinal plant by employing silica gel column chromatography and are characterized by NMR techniques. Antigastric cancer activity of these flavonoids was examined on AGS cell lines followed by cell cycle progression assay. In addition, pharmacophore-based screening and molecular dynamics of protein–ligand complex were carried out to identify potent scaffolds. The results showed that compounds 2 and 3 exhibited significant cytotoxic effect, whereas compound 1 showed moderate effect on AGS cells by inhibiting G2/M phase of cell cycle. Molecular docking analysis revealed that compound 2 has higher binding energies on human growth factor receptor-2 (HER2. The constructed pharmacophore models reveal that the compounds have more number of H-bond Acc/Don features which contribute to the inhibition of HER2 activity. By selecting these features, 34 hits were retrieved using the query compound 2. Molecular dynamic simulations (MDS of protein–ligand complexes demonstrated conspicuous

  16. Comprehensive processing of high-throughput small RNA sequencing data including quality checking, normalization, and differential expression analysis using the UEA sRNA Workbench.

    Science.gov (United States)

    Beckers, Matthew; Mohorianu, Irina; Stocks, Matthew; Applegate, Christopher; Dalmay, Tamas; Moulton, Vincent

    2017-06-01

    Recently, high-throughput sequencing (HTS) has revealed compelling details about the small RNA (sRNA) population in eukaryotes. These 20 to 25 nt noncoding RNAs can influence gene expression by acting as guides for the sequence-specific regulatory mechanism known as RNA silencing. The increase in sequencing depth and number of samples per project enables a better understanding of the role sRNAs play by facilitating the study of expression patterns. However, the intricacy of the biological hypotheses coupled with a lack of appropriate tools often leads to inadequate mining of the available data and thus, an incomplete description of the biological mechanisms involved. To enable a comprehensive study of differential expression in sRNA data sets, we present a new interactive pipeline that guides researchers through the various stages of data preprocessing and analysis. This includes various tools, some of which we specifically developed for sRNA analysis, for quality checking and normalization of sRNA samples as well as tools for the detection of differentially expressed sRNAs and identification of the resulting expression patterns. The pipeline is available within the UEA sRNA Workbench, a user-friendly software package for the processing of sRNA data sets. We demonstrate the use of the pipeline on a H. sapiens data set; additional examples on a B. terrestris data set and on an A. thaliana data set are described in the Supplemental Information A comparison with existing approaches is also included, which exemplifies some of the issues that need to be addressed for sRNA analysis and how the new pipeline may be used to do this. © 2017 Beckers et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  17. Determination of sulfur in human hair using high resolution continuum source graphite furnace molecular absorption spectrometry and its correlation with total protein and albumin

    Science.gov (United States)

    Ozbek, Nil; Baysal, Asli

    2017-04-01

    Human hair is a valuable contributor for biological monitoring. It is an information storage point to assess the effects of environmental, nutritional or occupational sources on the body. Human proteins, amino acids or other compounds are among the key components to find the sources of different effects or disorders in the human body. Sulfur is a significant one of these compounds, and it has great affinity to some metals and compounds. This property of the sulfur affects the human health positively or negatively. In this manuscript, sulfur was determined in hair samples of autistic and age-match control group children via molecular absorption of CS using a high-resolution continuum source graphite furnace atomic absorption spectrometer. For this purpose, hair samples were appropriately washed and dried at 75 °C. Then samples were dissolved in microwave digestion using HNO3 for sulfur determination. Extraction was performed with HCl hydrolysation by incubation for 24 h at 110 °C for total protein and albumin determination. The validity of the method for the sulfur determination was tested using hair standard reference materials. The results were in the uncertainty limits of the certified values at 95% confidence level. Finally correlation of sulfur levels of autistic children's hair with their total protein and albumin levels were done.

  18. Evaluation of distribution and sources of sewage molecular marker (LABs) in selected rivers and estuaries of Peninsular Malaysia.

    Science.gov (United States)

    Magam, Sami M; Zakaria, Mohamad Pauzi; Halimoon, Normala; Aris, Ahmad Zaharin; Kannan, Narayanan; Masood, Najat; Mustafa, Shuhaimi; Alkhadher, Sadeq; Keshavarzifard, Mehrzad; Vaezzadeh, Vahab; Sani, Muhamad S A; Latif, Mohd Talib

    2016-03-01

    This is the first extensive report on linear alkylbenzenes (LABs) as sewage molecular markers in surface sediments collected from the Perlis, Kedah, Merbok, Prai, and Perak Rivers and Estuaries in the west of Peninsular Malaysia. Sediment samples were extracted, fractionated, and analyzed using gas chromatography mass spectrometry (GC-MS). The concentrations of total LABs ranged from 68 to 154 (Perlis River), 103 to 314 (Kedah River), 242 to 1062 (Merbok River), 1985 to 2910 (Prai River), and 217 to 329 ng g(-1) (Perak River) dry weight (dw). The highest levels of LABs were found at PI3 (Prai Estuary) due to the rapid industrialization and population growth in this region, while the lowest concentrations of LABs were found at PS1 (upstream of Perlis River). The LABs ratio of internal to external isomers (I/E) in this study ranged from 0.56 at KH1 (upstream of Kedah River) to 1.35 at MK3 (Merbok Estuary) indicating that the rivers receive raw sewage and primary treatment effluents in the study area. In general, the results of this paper highlighted the necessity of continuation of water treatment system improvement in Malaysia.

  19. Genome Size, Molecular Phylogeny, and Evolutionary History of the Tribe Aquilarieae (Thymelaeaceae, the Natural Source of Agarwood

    Directory of Open Access Journals (Sweden)

    Azman H. Farah

    2018-05-01

    Full Text Available The tribe Aquilarieae of the family Thymelaeaceae consists of two genera, Aquilaria and Gyrinops, with a total of 30 species, distributed from northeast India, through southeast Asia and the south of China, to Papua New Guinea. They are an important botanical resource for fragrant agarwood, a prized product derived from injured or infected stems of these species. The aim of this study was to estimate the genome size of selected Aquilaria species and comprehend the evolutionary history of Aquilarieae speciation through molecular phylogeny. Five non-coding chloroplast DNA regions and a nuclear region were sequenced from 12 Aquilaria and three Gyrinops species. Phylogenetic trees constructed using combined chloroplast DNA sequences revealed relationships of the studied 15 members in Aquilarieae, while nuclear ribosomal DNA internal transcribed spacer (ITS sequences showed a paraphyletic relationship between Aquilaria species from Indochina and Malesian. We exposed, for the first time, the estimated divergence time for Aquilarieae speciation, which was speculated to happen during the Miocene Epoch. The ancestral split and biogeographic pattern of studied species were discussed. Results showed no large variation in the 2C-values for the five Aquilaria species (1.35–2.23 pg. Further investigation into the genome size may provide additional information regarding ancestral traits and its evolution history.

  20. Molecular characterization and potential sources of aqueous humor bacterial contamination during phacoemulsification with intraocular lens implantation in dogs.

    Science.gov (United States)

    Lacerda, Luciana C C; de Souza-Pollo, Andressa; Padua, Ivan Ricardo M; Conceição, Luciano F; da Silveira, Camila P Balthazar; Silva, Germana A; Maluta, Renato P; Laus, José L

    2018-01-01

    Bacterial contamination of the anterior chamber during cataract surgery is one of the main responsible for endophthalmitis postoperative. Phacoemulsification is a less invasive technique for cataract treatment, although it does not exclude the possibility of contamination. In this study, bacterial contaminants of aqueous humor collected pre- and post-phacoemulsification with intraocular lens implantation (IOL) of twenty dogs were identified. As the conjunctival microbiota constitute a significant source of anterior chamber contamination, bacterial isolates from aqueous humor were genetically compared with those present in the conjunctival surface of the patients. Three dogs presented bacterial growth in both aqueous humor and conjunctival surface samples. Bacterial isolates from these samples were grouped according to their genetic profiles by repetitive-element PCR (rep-PCR) and their representatives were identified by 16S rRNA sequencing. Isolates from conjunctival surface were identified as Enterobacter spp., Staphylococcus spp. and S. aureus; and from aqueous humor samples as Enterobacter spp., Pantoea spp., Streptococcus spp. and Staphylococcus spp., respectively in decreasing order of prevalence. According to the rep-PCR analysis, 16.6% of Enterobacter spp. isolates from conjunctival surface were genetically similar to those from aqueous humor. The rest of isolates encountered in aqueous humor were genetically distinct from those of conjunctival surface. The significant genetic diversity of bacterial isolates found in the aqueous humor samples after surgery denoted the possibility of anterior chamber contamination during phacoemulsification by bacteria not only from conjunctival surface but also from different sources related to surgical environment. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Versatile piezoelectric pulsed molecular beam source for gaseous compounds and organic molecules with femtomole accuracy for UHV and surface science applications

    International Nuclear Information System (INIS)

    Schiesser, Alexander; Schaefer, Rolf

    2009-01-01

    This note describes the construction of a piezoelectric pulsed molecular beam source based upon a design presented in an earlier work [D. Proch and T. Trickl, Rev. Sci. Instrum. 60, 713 (1988)]. The design features significant modifications that permit the determination of the number of molecules in a beam pulse with an accuracy of 1x10 11 molecules per pulse. The 21 cm long plunger-nozzle setup allows the molecules to be brought to any point of the UHV chamber with very high intensity. Furthermore, besides typical gaseous compounds, also smaller organic molecules with a vapor pressure higher than 0.1 mbar at room temperature may serve as feed material. This makes the new design suitable for various applications in chemical and surface science studies.

  2. High-temperature operation of self-assembled GaInNAs/GaAsN quantum-dot lasers grown by solid-source molecular-beam epitaxy

    International Nuclear Information System (INIS)

    Liu, C.Y.; Yoon, S.F.; Sun, Z.Z.; Yew, K.C.

    2006-01-01

    Self-assembled GaInNAs/GaAsN single layer quantum-dot (QD) lasers grown using solid-source molecular-beam epitaxy have been fabricated and characterized. Temperature-dependent measurements have been carried out on the GaInNAs QD lasers. The lowest obtained threshold current density in this work is ∼1.05 kA/cm 2 from a GaInNAs QD laser (50x1700 μm 2 ) at 10 deg. C. High-temperature operation up to 65 deg. C was also demonstrated from an unbonded GaInNAs QD laser (50x1060 μm 2 ), with high characteristic temperature of 79.4 K in the temperature range of 10-60 deg. C

  3. Investigation of chemical modifiers for sulfur determination in diesel fuel samples by high-resolution continuum source graphite furnace molecular absorption spectrometry using direct analysis

    Energy Technology Data Exchange (ETDEWEB)

    Huber, Charles S. [Instituto Federal Sul-rio-grandense, Câmpus Pelotas, Pelotas, RS (Brazil); Universidade Federal do Rio Grande do Sul, Instituto de Química, Porto Alegre, RS (Brazil); Vale, Maria Goreti R. [Universidade Federal do Rio Grande do Sul, Instituto de Química, Porto Alegre, RS (Brazil); Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Welz, Bernhard [Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Universidade Federal de Santa Catarina, Departamento de Química, Florianópolis, SC (Brazil); Andrade, Jailson B. [Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Dessuy, Morgana B., E-mail: mbdessuy@ufrgs.br [Universidade Federal do Rio Grande do Sul, Instituto de Química, Porto Alegre, RS (Brazil); Instituto Nacional de Ciência e Tecnologia do CNPq, INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil)

    2015-06-01

    High-resolution continuum source graphite furnace molecular absorption spectrometry has been applied for sulfur determination in diesel fuel. The sharp rotational lines of the carbon monosulfide molecule (formed during the vaporization step) were used to measure the absorbance. The analytical line at 258.056 nm was monitored using the sum of three pixels. Different chemical modifiers were investigated and the mixture of palladium and magnesium was used as chemical modifier in combination with iridium as permanent modifier. L-Cysteine was chosen as sulfur standard and the calibration was done against aqueous standard solutions. The proposed method was applied for the analyses of four diesel samples: two S10 samples and two S500 samples. The trueness of the method was checked with a certified reference material (CRM) of sulfur in diesel fuel (NIST 2724b). Accurate results, for samples and CRM, were achieved after a dilution with propan-1-ol. The following figures of merit were obtained: characteristic mass of 17 ± 3 ng, limit of detection and limit of quantification of 1.4 mg kg{sup −1} and 4.7 mg kg{sup −1}, respectively. - Highlights: • Ir, Ru and Zr were investigated as permanent modifiers. • Ca, Mg, Pd and Pd/Mg were investigated as modifiers in solution. • Indirect determination of sulfur monitoring the molecular absorbance of the CS • Direct analysis of diesel samples using a dilution in propan-1-ol.

  4. In silico carbon molecular beam epitaxial growth of graphene on the h-BN substrate: carbon source effect on van der Waals epitaxy

    Science.gov (United States)

    Lee, Jonghoon; Varshney, Vikas; Park, Jeongho; Farmer, Barry L.; Roy, Ajit K.

    2016-05-01

    Against the presumption that hexagonal boron-nitride (h-BN) should provide an ideal substrate for van der Waals (vdW) epitaxy to grow high quality graphene films, carbon molecular beam epitaxy (CMBE) techniques using solid carbon sublimation have reported relatively poor quality of the graphene. In this article, the CMBE growth of graphene on the h-BN substrate is numerically studied in order to identify the effect of the carbon source on the quality of the graphene film. The carbon molecular beam generated by the sublimation of solid carbon source materials such as graphite and glassy carbon is mostly composed of atomic carbon, carbon dimers and carbon trimers. Therefore, the graphene film growth becomes a complex process involving various deposition characteristics of a multitude of carbon entities. Based on the study of surface adsorption and film growth characteristics of these three major carbon entities comprising graphite vapour, we report that carbon trimers convey strong traits of vdW epitaxy prone to high quality graphene growth, while atomic carbon deposition is a surface-reaction limited process accompanied by strong chemisorption. The vdW epitaxial behaviour of carbon trimers is found to be substantial enough to nucleate and develop into graphene like planar films within a nanosecond of high flux growth simulation, while reactive atomic carbons tend to impair the structural integrity of the crystalline h-BN substrate upon deposition to form an amorphous interface between the substrate and the growing carbon film. The content of reactive atomic carbons in the molecular beam is suspected to be the primary cause of low quality graphene reported in the literature. A possible optimization of the molecular beam composition towards the synthesis of better quality graphene films is suggested.Against the presumption that hexagonal boron-nitride (h-BN) should provide an ideal substrate for van der Waals (vdW) epitaxy to grow high quality graphene films, carbon

  5. Get Your Atoms in Order--An Open-Source Implementation of a Novel and Robust Molecular Canonicalization Algorithm.

    Science.gov (United States)

    Schneider, Nadine; Sayle, Roger A; Landrum, Gregory A

    2015-10-26

    Finding a canonical ordering of the atoms in a molecule is a prerequisite for generating a unique representation of the molecule. The canonicalization of a molecule is usually accomplished by applying some sort of graph relaxation algorithm, the most common of which is the Morgan algorithm. There are known issues with that algorithm that lead to noncanonical atom orderings as well as problems when it is applied to large molecules like proteins. Furthermore, each cheminformatics toolkit or software provides its own version of a canonical ordering, most based on unpublished algorithms, which also complicates the generation of a universal unique identifier for molecules. We present an alternative canonicalization approach that uses a standard stable-sorting algorithm instead of a Morgan-like index. Two new invariants that allow canonical ordering of molecules with dependent chirality as well as those with highly symmetrical cyclic graphs have been developed. The new approach proved to be robust and fast when tested on the 1.45 million compounds of the ChEMBL 20 data set in different scenarios like random renumbering of input atoms or SMILES round tripping. Our new algorithm is able to generate a canonical order of the atoms of protein molecules within a few milliseconds. The novel algorithm is implemented in the open-source cheminformatics toolkit RDKit. With this paper, we provide a reference Python implementation of the algorithm that could easily be integrated in any cheminformatics toolkit. This provides a first step toward a common standard for canonical atom ordering to generate a universal unique identifier for molecules other than InChI.

  6. adLIMS: a customized open source software that allows bridging clinical and basic molecular research studies.

    Science.gov (United States)

    Calabria, Andrea; Spinozzi, Giulio; Benedicenti, Fabrizio; Tenderini, Erika; Montini, Eugenio

    2015-01-01

    Many biological laboratories that deal with genomic samples are facing the problem of sample tracking, both for pure laboratory management and for efficiency. Our laboratory exploits PCR techniques and Next Generation Sequencing (NGS) methods to perform high-throughput integration site monitoring in different clinical trials and scientific projects. Because of the huge amount of samples that we process every year, which result in hundreds of millions of sequencing reads, we need to standardize data management and tracking systems, building up a scalable and flexible structure with web-based interfaces, which are usually called Laboratory Information Management System (LIMS). We started collecting end-users' requirements, composed of desired functionalities of the system and Graphical User Interfaces (GUI), and then we evaluated available tools that could address our requirements, spanning from pure LIMS to Content Management Systems (CMS) up to enterprise information systems. Our analysis identified ADempiere ERP, an open source Enterprise Resource Planning written in Java J2EE, as the best software that also natively implements some highly desirable technological advances, such as the high usability and modularity that grants high use-case flexibility and software scalability for custom solutions. We extended and customized ADempiere ERP to fulfil LIMS requirements and we developed adLIMS. It has been validated by our end-users verifying functionalities and GUIs through test cases for PCRs samples and pre-sequencing data and it is currently in use in our laboratories. adLIMS implements authorization and authentication policies, allowing multiple users management and roles definition that enables specific permissions, operations and data views to each user. For example, adLIMS allows creating sample sheets from stored data using available exporting operations. This simplicity and process standardization may avoid manual errors and information backtracking, features

  7. Self-assembled GaInNAs/GaAsN quantum dot lasers: solid source molecular beam epitaxy growth and high-temperature operation

    Directory of Open Access Journals (Sweden)

    Yoon SF

    2006-01-01

    Full Text Available AbstractSelf-assembled GaInNAs quantum dots (QDs were grown on GaAs (001 substrate using solid-source molecular-beam epitaxy (SSMBE equipped with a radio-frequency nitrogen plasma source. The GaInNAs QD growth characteristics were extensively investigated using atomic-force microscopy (AFM, photoluminescence (PL, and transmission electron microscopy (TEM measurements. Self-assembled GaInNAs/GaAsN single layer QD lasers grown using SSMBE have been fabricated and characterized. The laser worked under continuous wave (CW operation at room temperature (RT with emission wavelength of 1175.86 nm. Temperature-dependent measurements have been carried out on the GaInNAs QD lasers. The lowest obtained threshold current density in this work is ∼1.05 kA/cm2from a GaInNAs QD laser (50 × 1,700 µm2 at 10 °C. High-temperature operation up to 65 °C was demonstrated from an unbonded GaInNAs QD laser (50 × 1,060 µm2, with high characteristic temperature of 79.4 K in the temperature range of 10–60 °C.

  8. Molecular assays for targeting human and bovine enteric viruses in coastal waters and their application for library-independent source tracking

    Science.gov (United States)

    Fong, T.-T.; Griffin, Dale W.; Lipp, E.K.

    2005-01-01

    Rapid population growth and urban development along waterways and coastal areas have led to decreasing water quality. To examine the effects of upstream anthropogenic activities on microbiological water quality, methods for source-specific testing are required. In this study, molecular assays targeting human enteroviruses (HEV), bovine enteroviruses (BEV), and human adenoviruses (HAdV) were developed and used to identify major sources of fecal contamination in the lower Altamaha River, Georgia. Two-liter grab samples were collected monthly from five tidally influenced stations between July and December 2002. Samples were analyzed by reverse transcription- and nested-PCR. PCR results were confirmed by dot blot hybridization. Eleven and 17 of the 30 surface water samples tested positive for HAdV and HEV, respectively. Two-thirds of the samples tested positive for either HEV or HAdV, and the viruses occurred simultaneously in 26% of samples. BEV were detected in 11 of 30 surface water samples. Binary logistic regression analysis showed that the presence of both human and bovine enteric viruses was not significantly related to either fecal coliform or total coliform levels. The presence of these viruses was directly related to dissolved oxygen and streamflow but inversely related to water temperature, rainfall in the 30 days preceding sampling, and chlorophyll-?? concentrations. The stringent host specificity of enteric viruses makes them good library-independent indicators for identification of water pollution sources. Viral pathogen detection by PCR is a highly sensitive and easy-to-use tool for rapid assessment of water quality and fecal contamination when public health risk characterization is not necessary. Copyright ?? 2005, American Society for Microbiology. All Rights Reserved.

  9. Ten years of surveillance of the Yulong plague focus in China and the molecular typing and source tracing of the isolates.

    Science.gov (United States)

    Wang, Peng; Shi, Liyuan; Zhang, Fuxin; Guo, Ying; Zhang, Zhikai; Tan, Hongli; Cui, Zhigang; Ding, Yibo; Liang, Ying; Liang, Yun; Yu, Dongzheng; Xu, Jianguo; Li, Wei; Song, Zhizhong

    2018-03-01

    Plague, caused by Yersinia pestis, was classified as a reemerging infectious disease by the World Health Organization. The five human pneumonic plague cases in Yulong County in 2005 gave rise to the discovery of a Yulong plague focus in Yunnan province, China. Thereafter, continuous wild rodent plague (sylvatic plague) was identified as the main plague reservoir of this focus. In this study, the epizootics in Yulong focus were described, and three molecular typing methods, including the different region (DFR) analysis, clustered regularly interspaced short palindromic repeats (CRISPRs), and the multiple-locus variable number of tandem repeats (VNTR) analysis (MLVA) (14+12), were used for the molecular typing and source tracing of Y. pestis isolates in the Yulong plague focus. Simultaneously, several isolates from the vicinity of Yunnan were used as controls. The results showed that during the 10-year period from 2006 to 2016, an animal plague epidemic occurred in 6 of those years, and 5 villages underwent an animal plague epidemic within a 30-km2 area of the Yulong plague focus. Searching for dead mice was the most effective monitoring method in this plague focus. No positive sample has been found in 6937 captured live rodents thus far, suggesting that the virulence of strains in the Yulong plague focus is stronger and the survival time of mice is shorter after infection. Strains from Lijiang, Sichuan and Tibet were of the same complex based on a typing analysis of DFR and CRISPR. The genetic relationship of Y. pestis illustrated by MLVA "14+12" demonstrates that Tibet and Sichuan strains evolved from the strains 1.IN2 (Qinghai, 1970 and Tibet, 1976), and Lijiang strains are closer to Batang strains (Batang County in Sichuan province, 2011, Himalaya marmot plague foci) in terms of genetic or phylogenic relationships. In conclusion, we have a deeper understanding of this new plague focus throughout this study, which provides a basis for effective prevention and

  10. Long Carbon Chains in the Warm Carbon-chain-chemistry Source L1527: First Detection of C7H in Molecular Clouds

    Science.gov (United States)

    Araki, Mitsunori; Takano, Shuro; Sakai, Nami; Yamamoto, Satoshi; Oyama, Takahiro; Kuze, Nobuhiko; Tsukiyama, Koichi

    2017-09-01

    Long carbon-chain molecules were searched for toward the low-mass star-forming region L1527, which is a prototypical source of warm carbon-chain chemistry (WCCC), using the 100 m Green Bank Telescope. Long carbon-chain molecules, C7H (2Π1/2), C6H (2Π3/2 and 2Π1/2), CH3C4H, and C6H2 (cumulene carbene, CCCCCCH2), and cyclic species of C3H and C3H2O were detected. In particular, C7H was detected for the first time in molecular clouds. The column density of C7H is determined to be 6 × 1010 cm-2. The column densities of the carbon-chain molecules including CH3C4H and C6H in L1527 relative to those in the starless dark cloud Taurus Molecular Cloud-1 Cyanopolyyne Peak (TMC-1 CP) tend to be systematically lower for long carbon-chain lengths. However, the column densities of C7H and C6H2 do not follow this trend and are found to be relatively abundant in L1527. This result implies that these long carbon-chain molecules are remnants of the cold starless phase. The results—that both the remnants and WCCC products are observed toward L1527—are consistent with the suggestion that the protostar can also be born in the parent core at a relatively early stage in the chemical evolution.

  11. Contribution to the study of the molecular scattering of light. Use of a laser as light source (1963); Contribution a l'etude de la diffusion moleculaire de la lumiere. Utilisation d'un laser comme source lumineuse (1963)

    Energy Technology Data Exchange (ETDEWEB)

    Slama, L [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

    1963-07-01

    The experiments of the molecular scattering of light have been repeated using a ruby laser as a light source. The angular distribution of the scattered light intensity has been measured when the electric vector of the incident beam is either in the plane of observation or perpendicular to that plane. In the first case a good agreement with the Rayleigh theory has been found but this is not true in the second case. The differential cross sections for scattering have been measured for various gases. The values found are two or three times larger than the ones deduced from the classical theory. The possible effect of a variation of the beam intensity upon the linearity of the scattering process has been looked for. (author) [French] Les experiences sur la diffusion moleculaire de la lumiere ont ete reprises en utilisant un laser a rubis comme source lumineuse. La distribution angulaire de l'intensite diffusee a ete mesuree dans le cas ou le vecteur electrique de l'onde lumineuse incidente est soit dans le plan, soit perpendiculaire a ce plan. Dans le premier cas un bon accord est observe avec la theorie de Rayleigh, ce qui n'est plus vrai dans le second cas. Des sections efficaces differentielles de diffusion ont ete mesurees pour differents gaz. Les valeurs trouvees sont 2 a 3 fois plus grandes que celles prevues par la theorie classique. On a recherche enfin l'effet d'une variation d'intensite du faisceau du laser sur la linearite du phenomene de diffusion. (auteur)

  12. Metabolomics Workbench (MetWB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Metabolomics Program's Data Repository and Coordinating Center (DRCC), housed at the San Diego Supercomputer Center (SDSC), University of California, San Diego,...

  13. Gas-source molecular beam epitaxy of Si(111) on Si(110) substrates by insertion of 3C-SiC(111) interlayer for hybrid orientation technology

    Energy Technology Data Exchange (ETDEWEB)

    Bantaculo, Rolando, E-mail: rolandobantaculo@yahoo.com; Saitoh, Eiji; Miyamoto, Yu; Handa, Hiroyuki; Suemitsu, Maki

    2011-11-01

    A method to realize a novel hybrid orientations of Si surfaces, Si(111) on Si(110), has been developed by use of a Si(111)/3C-SiC(111)/Si(110) trilayer structure. This technology allows us to use the Si(111) portion for the n-type and the Si(110) portion for the p-type channels, providing a solution to the current drive imbalance between the two channels confronted in Si(100)-based complementary metal oxide semiconductor (CMOS) technology. The central idea is to use a rotated heteroepitaxy of 3C-SiC(111) on Si(110) substrate, which occurs when a 3C-SiC film is grown under certain growth conditions. Monomethylsilane (SiH{sub 3}-CH{sub 3}) gas-source molecular beam epitaxy (GSMBE) is used for this 3C-SiC interlayer formation while disilane (Si{sub 2}H{sub 6}) is used for the top Si(111) layer formation. Though the film quality of the Si epilayer leaves a lot of room for betterment, the present results may suffice to prove its potential as a new technology to be used in the next generation CMOS devices.

  14. Determination of bromide in aqueous solutions via the TlBr molecule using high-resolution continuum source graphite furnace molecular absorption spectrometry

    Science.gov (United States)

    Cacho, Frantisek; Machynak, Lubomir; Nemecek, Martin; Beinrohr, Ernest

    2018-06-01

    The paper describes the determination of bromide by evaluating the molecular absorption of thallium mono-bromide (TlBr) at the rotational line at 342.9815 nm by making use a high-resolution continuum source graphite furnace atomic absorption spectrometer. The effects of variables such as the wavelength, graphite furnace program, amount of Tl and the use of a modifier were investigated and optimized. Various chemical modifiers have been studied, such as Pd, Mg, Ag and a mixture of Pd/Mg. It was found that best results were obtained by using Ag which prevents losses of bromide during pyrolysis step through precipitation of bromide as AgBr. In this way, a maximum pyrolysis temperature of 400 °C could be used. The optimum molecule forming temperature was found to be 900 °C. Bromide concentrations in various water samples (CRM, bottled drinking water and tap water) were determined. The quantification was made by both linear calibration and standard addition techniques. The results were matched well those of the reference method. The calibration curve was linear in the range between 1 and 1000 ng Br with a correlation coefficient R = 0.999. The limit of detection and characteristic mass of the method were 0.3 ng and 4.4 ng of Br.

  15. Microstructures of GaN1-xPx layers grown on (0001) GaN substrates by gas source molecular beam epitaxy

    Science.gov (United States)

    Seong, Tae-Yeon; Bae, In-Tae; Choi, Chel-Jong; Noh, D. Y.; Zhao, Y.; Tu, C. W.

    1999-03-01

    Transmission electron microscope (TEM), transmission electron diffraction (TED), and synchrotron x-ray diffraction (XRD) studies have been performed to investigate microstructural behavior of gas source molecular beam epitaxial GaN1-xPx layers grown on (0001) GaN/sapphire at temperatures (Tg) in the range 500-760 °C. TEM, TED, and XRD results indicate that the samples grown at Tg⩽600 °C undergo phase separation resulting in a mixture of GaN-rich and GaP-rich GaNP with zinc-blende structure. However, the samples grown at Tg⩾730 °C are found to be binary zinc-blende GaN(P) single crystalline materials. As for the 500 °C layer, the two phases are randomly oriented and distributed, whereas the 600 °C layer consists of phases that are elongated and inclined by 60°-70° clockwise from the [0001]α-GaN direction. The samples grown at Tg⩾730 °C are found to consist of two types of microdomains, namely, GaN(P)I and GaN(P)II; the former having twin relation to the latter.

  16. Determination of Chlorine in Milk via Molecular Absorption of SrCl Using High-Resolution Continuum Source Graphite Furnace Atomic Absorption Spectrometry.

    Science.gov (United States)

    Ozbek, Nil; Akman, Suleyman

    2016-07-20

    Total chlorine in milk was determined via the molecular absorption of diatomic strontium monochloride at 635.862 nm using high-resolution continuum source graphite furnace atomic absorption spectrometry. The effects of coating the graphite furnace, using different modifiers, amount of molecule-forming element, and different calibrants were investigated and optimized. Chlorine concentrations in milk samples were determined in a Zr-coated graphite furnace using 25 μg of Sr as the molecule-forming reagent and applying a pyrolysis temperature of 600 °C and a molecule-forming temperature of 2300 °C. Linearity was maintained up to 500 μg mL(-1) of Cl. The method was tested by analyzing a certified reference wastewater. The results were in the uncertainty limits of the certified value. The limit of detection of the method was 1.76 μg mL(-1). The chlorine concentrations in various cow milk samples taken from the market were found in the range of 588-1472 mg L(-1).

  17. Modelling, Design, Growth and Characterization of Strain Balanced Quantum Cascade Lasers (3-11mum), grown by Gas Source Molecular Beam Epitaxy

    Science.gov (United States)

    Bandyopadhyay, Neelanjan

    Quantum Cascade Laser (QCL) is a compact room temperature (RT) source of mid-infrared radiation, which can be used for spectroscopic detection of trace amount of chemicals. The mid-infrared spectral range between (3-11 microm), has a dense array of absorption lines of numerous molecules, due to the presence of fundamental vibrational modes. The goal of this thesis can be subdivided into two parts. Firstly, short wavelength QCLs, emitting below 4microm, perform poorly at RT, due to inter-valley Gamma --- L carrier scattering, carrier escape to the continuum, heat removal from the core region at high power density corresponding to short wavelength operation, and large interface scattering due to highly strained materials. Secondly, it is desirable to have a single QCL based source emitting between 6-10microm, which be used to detect multiple molecules having their peak absorptions far apart, inside this spectral range. However, gain bandwidth of a single core QCL is relatively small, so laser emission cannot be tuned over a wide spectral range. This thesis describes the working principle of a QCL based on superlattice transport, rate equations, scattering mechanism, and waveguide design. The choice of the material system for this work and the fundamentals of band structure engineering has been derived. Gas source molecular beam epitaxy - growth optimization and characterization is one of the most important features of this work, especially for short wavelength QCLs, and has been explained in depth. Different strategies for design of active region design of short wavelength QCL and heterogeneous broadband QCL has been explored. The major milestones, of this research was the world's first watt level continuous wave (CW), RT demonstration at 3.76 microm, which was followed by another milestone of the first CW, RT demonstration at 3.39microm and 3.55microm, and finally the elusive result of QCL emitting at CW, RT at a wavelength as short as lambda ~3microm, a record. In

  18. Determination of chlorine in food samples via the AlCl molecule using high-resolution continuum source molecular absorption spectrometry in a graphite furnace

    Energy Technology Data Exchange (ETDEWEB)

    Fechetia, Miriam; Tognon, Andre Luiz; Veiga, Marcia A.M.S. da, E-mail: mamsveiga@ffclrp.usp.br

    2012-05-15

    Determination of chlorine using the molecular absorption of aluminum mono-chloride (AlCl) at the 261.418 nm wavelength was accomplished by high-resolution continuum source molecular absorption spectrometry using a transversely heated graphite tube furnace with an integrated platform. For the analysis, 10 {mu}L of the sample followed by 10 {mu}L of a solution containing Al-Ag-Sr modifier, (1 g L{sup -1} each), were directly injected onto the platform. A spectral interference due to the use of Al-Ag-Sr as mixed modifier was easily corrected by the least-squares algorithm present in the spectrometer software. The pyrolysis and vaporization temperatures were 500 Degree-Sign C and 2200 Degree-Sign C, respectively. To evaluate the feasibility of a simple procedure for the determination of chlorine in food samples present in our daily lives, two different digestion methods were applied, namely (A) an acid digestion method using HNO{sub 3} only at room temperature, and (B) a digestion method with Ag, HNO{sub 3} and H{sub 2}O{sub 2}, where chlorine is precipitated as a low-solubility salt (AgCl), which is then dissolved with ammonia solution. The experimental results obtained with method B were in good agreement with the certified values and demonstrated that the proposed method is more accurate than method A. This is because the formation of silver chloride prevented analyte losses by volatilization. The limit of detection (LOD, 3{sigma}/s) for Cl in methods A and B was 18 {mu}g g{sup -1} and 9 {mu}g g{sup -1}, respectively, 1.7 and 3.3 times lower compared to published work using inductively coupled plasma optical emission spectrometry, and absolute LODs were 2.4 and 1.2 ng, respectively. - Highlights: Black-Right-Pointing-Pointer HR-CS MAS as technique for Cl determination via AlCl molecule Black-Right-Pointing-Pointer Spectral interference was corrected by the least-squares algorithm. Black-Right-Pointing-Pointer Chorine precipitation as AgCl prevents Cl losses during

  19. An undulator based high flux and high resolution beamline for atomic, molecular and optical science (AMOS) research at INDUS-2 synchrotron radiation source (SRS)

    International Nuclear Information System (INIS)

    Das, Asim Kumar; Rajasekhar, B.N.; Sahoo, N.K.

    2014-08-01

    A dedicated UV-VUV and soft X-ray beamline to provide several new research opportunities in Photon induced processes in the energy range of 6-250 eV for Atomic Molecular and Optical Science (AMOS) research, a domain still less explored both at national as well international level, has been proposed by Atomic and Molecular Physics Division, BARC. This beamline will use a planar permanent magnet (PPM) undulator based on Indus-2 Synchrotron Radiation Source (SRS), a 2.5 GeV third generation electron storage ring at RRCAT, Indore, India and is expected to offer a variety of opportunities for more advanced and sustained investigations for AMOS research. A plane mirror and a toroidal mirror are used as the pre-focusing optics of the AMOS beamline. A varied line spacing plane grating monochromator (VLSPGM) in a converging beam, constant included angle mode containing one toroidal focusing mirror and four interchangeable gratings is to be used to cover the energy range of 6 to 250 eV and obtain resolving powers ∼10 4 and intensity ∼10 12 ph/s at the sample position. A toroidal mirror is used to focus the diverging monochromatic light from the monochromator at a distance of 150 cm with a 1:1 magnification. As the first step towards the beamline optics design, the evaluation of the PPM undulator radiation characteristics relevant to beamline design has been performed using the Indus-2 SRS parameters in the long straight section of the ring, PPM undulator parameters, and the empirical expressions available in literature. The software resources such as XOPS, ESRF, France and SPECTRA, Photon factory, Japan have been used for detailed modelling and verification of the empirical computations. Beamline layout preparation, optimization, imaging performance evaluation, and resolving power calculations for ideal beamline optics are carried out using SHADOWVUI, an extension of XOPS software resource. A new mounting of the optical components in the monochromator has been proposed

  20. A simple and fast method for assessment of the nitrogen–phosphorus–potassium rating of fertilizers using high-resolution continuum source atomic and molecular absorption spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Bechlin, Marcos André; Fortunato, Felipe Manfroi; Moutinho da Silva, Ricardo; Ferreira, Edilene Cristina; Gomes Neto, José Anchieta, E-mail: anchieta@iq.unesp.br

    2014-11-01

    The determination of N, P, and K in fertilizers by high-resolution continuum source flame atomic and molecular absorption spectrometry is proposed. Under optimized conditions, measurements of the diatomic molecules NO and PO at 215.360 and 247.620 nm, respectively, and K using the wing of the alternative line at 404.722 nm allowed calibration curves to be constructed in the ranges 500–5000 mg L{sup −1} N (r = 0.9994), 100–2000 mg L{sup −1} P (r = 0.9946), and 100–2500 mg L{sup −1} K (r = 0.9995). Commercial fertilizers were analyzed by the proposed method and the concentrations of N, P, and K were found to be in agreement with those obtained by Kjeldahl, spectrophotometric, and flame atomic emission spectrometry methods, respectively, at a 95% confidence level (paired t-test). A phosphate rock certified reference material (CRM) was analyzed and the results for P and K were in agreement with the reference values. Recoveries from spiked CRM were in the ranges 97–105% (NO{sub 3}{sup −}-N), 95–103% (NH{sub 4}{sup +}-N), 93–103% (urea-N), 99–108% (P), and 99–102% (K). The relative standard deviations (n = 12) for N, P, and K were 6, 4, and 2%, respectively. - Highlights: • A single technique is proposed to analyze NPK fertilizer. • HR-CS FAAS is proposed for the first time for N, P and K determination in fertilizers. • The method employs the same sample preparation and dilution for the three analytes. • Addition of H{sub 2}O{sub 2} allows analysis of fertilizers with different nitrogen species. • Proposal provides advantages over traditional methods in terms of cost and time.

  1. Calcium impurity as a source of non-radiative recombination in (In,Ga)N layers grown by molecular beam epitaxy

    KAUST Repository

    Young, E. C.; Grandjean, N.; Mates, T. E.; Speck, J. S.

    2016-01-01

    Ca as an unintentional impurity has been investigated in III-nitride layers grown by molecular beam epitaxy (MBE). It is found that Ca originates from the substrate surface, even if careful cleaning and rinsing procedures are applied. The initial Ca surface coverage is ∼1012 cm−2, which is consistent with previous reports on GaAs and silicon wafers. At the onset of growth, the Ca species segregates at the growth front while incorporating at low levels. The incorporation rate is strongly temperature dependent. It is about 0.03% at 820 °C and increases by two orders of magnitude when the temperature is reduced to 600 °C, which is the typical growth temperature for InGaN alloy. Consequently, [Ca] is as high as 1018 cm−3 in InGaN/GaN quantum well structures. Such a huge concentration might be detrimental for the efficiency of light emitting diodes (LEDs) if one considers that Ca is potentially a source of Shockley-Read-Hall (SRH) defects. We thus developed a specific growth strategy to reduce [Ca] in the MBE grown LEDs, which consisted of burying Ca in a low temperature InGaN/GaN superlattice (SL) before the growth of the active region. Finally, two LED samples with and without an SL were fabricated. An increase in the output power by one order of magnitude was achieved when Ca was reduced in the LED active region, providing evidence for the role of Ca in the SRH recombination.

  2. A simple and fast method for assessment of the nitrogen–phosphorus–potassium rating of fertilizers using high-resolution continuum source atomic and molecular absorption spectrometry

    International Nuclear Information System (INIS)

    Bechlin, Marcos André; Fortunato, Felipe Manfroi; Moutinho da Silva, Ricardo; Ferreira, Edilene Cristina; Gomes Neto, José Anchieta

    2014-01-01

    The determination of N, P, and K in fertilizers by high-resolution continuum source flame atomic and molecular absorption spectrometry is proposed. Under optimized conditions, measurements of the diatomic molecules NO and PO at 215.360 and 247.620 nm, respectively, and K using the wing of the alternative line at 404.722 nm allowed calibration curves to be constructed in the ranges 500–5000 mg L −1 N (r = 0.9994), 100–2000 mg L −1 P (r = 0.9946), and 100–2500 mg L −1 K (r = 0.9995). Commercial fertilizers were analyzed by the proposed method and the concentrations of N, P, and K were found to be in agreement with those obtained by Kjeldahl, spectrophotometric, and flame atomic emission spectrometry methods, respectively, at a 95% confidence level (paired t-test). A phosphate rock certified reference material (CRM) was analyzed and the results for P and K were in agreement with the reference values. Recoveries from spiked CRM were in the ranges 97–105% (NO 3 − -N), 95–103% (NH 4 + -N), 93–103% (urea-N), 99–108% (P), and 99–102% (K). The relative standard deviations (n = 12) for N, P, and K were 6, 4, and 2%, respectively. - Highlights: • A single technique is proposed to analyze NPK fertilizer. • HR-CS FAAS is proposed for the first time for N, P and K determination in fertilizers. • The method employs the same sample preparation and dilution for the three analytes. • Addition of H 2 O 2 allows analysis of fertilizers with different nitrogen species. • Proposal provides advantages over traditional methods in terms of cost and time

  3. Calcium impurity as a source of non-radiative recombination in (In,Ga)N layers grown by molecular beam epitaxy

    KAUST Repository

    Young, E. C.

    2016-11-23

    Ca as an unintentional impurity has been investigated in III-nitride layers grown by molecular beam epitaxy (MBE). It is found that Ca originates from the substrate surface, even if careful cleaning and rinsing procedures are applied. The initial Ca surface coverage is ∼1012 cm−2, which is consistent with previous reports on GaAs and silicon wafers. At the onset of growth, the Ca species segregates at the growth front while incorporating at low levels. The incorporation rate is strongly temperature dependent. It is about 0.03% at 820 °C and increases by two orders of magnitude when the temperature is reduced to 600 °C, which is the typical growth temperature for InGaN alloy. Consequently, [Ca] is as high as 1018 cm−3 in InGaN/GaN quantum well structures. Such a huge concentration might be detrimental for the efficiency of light emitting diodes (LEDs) if one considers that Ca is potentially a source of Shockley-Read-Hall (SRH) defects. We thus developed a specific growth strategy to reduce [Ca] in the MBE grown LEDs, which consisted of burying Ca in a low temperature InGaN/GaN superlattice (SL) before the growth of the active region. Finally, two LED samples with and without an SL were fabricated. An increase in the output power by one order of magnitude was achieved when Ca was reduced in the LED active region, providing evidence for the role of Ca in the SRH recombination.

  4. Use of Residual Biomass from the Textile Industry as Carbon Source for Production of a Low-Molecular-Weight Xylanase from Aspergillus oryzae

    Directory of Open Access Journals (Sweden)

    Gilvan Caetano Duarte

    2012-10-01

    Full Text Available Pretreated dirty cotton residue (PDCR from the textile industry was used as an alternative carbon source for the submerged cultivation of Aspergillus oryzae and the production of xylanases. The filtered culture supernatant was fractionated by ultrafiltration followed by three chromatographic steps, which resulted in the isolation of a homogeneous low-molecular-weight xylanase (Xyl-O1 with a mass of 21.5 kDa as determined by sodium dodecyl sulfate-polyacrilamide gel electrophoresis (SDS-PAGE co-polymerized with 0.1% oat spelt xylan. Enzyme catalysis was the most efficient at 50 °C and pH 6.0. The Km values (mg·mL−1 for the soluble fraction of oat spelt and birchwood xylans were 10.05 and 3.34, respectively. Xyl-O1 was more stable in the presence of 5,5-dithio-bis-(2-nitrobenzoic acid (DTNB, 1,4-dithiothreitol (DTT, l-cysteine or β-mercaptoethanol, which increased the rate of catalysis by 40%, 14%, 40% or 37%, respectively. The enzyme stability was improved at pH 7.0 in the presence of 20 mM l-cysteine, with the retention of nearly 100% of the activity after 6 h at 50 °C. Xyl-O1 catalyzed the cleavage of internal β-1,4 linkages of the soluble substrates containing d-xylose residues, with a maximum efficiency of 33% for the hydrolysis of birchwood xylan after 12 h of incubation. Identification of the hydrolysis products by high-performance anion exchange chromatography coupled with pulsed amperometric detection (HPAEC-PAD indicated the predominance of the hydrolysis products X2-X6 during the first 12 h of incubation and the accumulation of higher xylooligomers after the elution of the last xylooligomer standard, xylohexaose.

  5. Ultrahigh B doping (≤1022 cm-3) during Si(001) gas-source molecular-beam epitaxy: B incorporation, electrical activation, and hole transport

    International Nuclear Information System (INIS)

    Glass, G.; Kim, H.; Desjardins, P.; Taylor, N.; Spila, T.; Lu, Q.; Greene, J. E.

    2000-01-01

    Si(001) layers doped with B concentrations C B between 1x10 17 and 1.2x10 22 cm -3 (24 at %) were grown on Si(001)2x1 at temperatures T s =500-850 degree sign C by gas-source molecular-beam epitaxy from Si 2 H 6 and B 2 H 6 . C B increases linearly with the incident precursor flux ratio J B 2 H 6 /J Si 2 H 6 and B is incorporated into substitutional electrically active sites at concentrations up to C B * (T s ) which, for T s =600 degree sign C, is 2.5x10 20 cm -3 . At higher B concentrations, C B increases faster than J B 2 H 6 /J Si 2 H 6 and there is a large and discontinuous decrease in the activated fraction of incorporated B. However, the total activated B concentration continues to increase and reaches a value of N B =1.3x10 21 cm -3 with C B =1.2x10 22 cm -3 . High-resolution x-ray diffraction (HR-XRD) and reciprocal space mapping measurements show that all films, irrespective of C B and T s , are fully strained. No B precipitates or misfit dislocations were detected by HR-XRD or transmission electron microscopy. The lattice constant in the film growth direction a (perpendicular sign) decreases linearly with increasing C B up to the limit of full electrical activation and continues to decrease, but nonlinearly, with C B >C B * . Room-temperature resistivity and conductivity mobility values are in good agreement with theoretical values for B concentrations up to C B =2.5x10 20 and 2x10 21 cm -3 , respectively. All results can be explained on the basis of a model which accounts for strong B surface segregation to the second-layer with a saturation coverage θ B,sat of 0.5 ML (corresponding to C B =C B * ). At higher C B (i.e., θ B >θ B,sat ), B accumulates in the upper layer as shown by thermally programmed desorption measurements, and a parallel incorporation channel becomes available in which B is incorporated into substitutional sites as B pairs that are electrically inactive but have a low charge-scattering cross section. (c) 2000 The American Physical

  6. Molecular phylogeny of Indo-Pacific carpenter ants (Hymenoptera: Formicidae, Camponotus) reveals waves of dispersal and colonization from diverse source areas

    Czech Academy of Sciences Publication Activity Database

    Clouse, R. M.; Janda, Milan; Blanchard, B.; Sharma, P.; Hoffmann, B. D.; Andersen, A. N.; Czekanski-Moir, J. E.; Krushelnycky, P.; Rabeling, C.; Wilson, E. O.; Economo, E. P.; Sarnat, E. M.; General, D. M.; Alpert, G. D.; Wheeler, W. C.

    2015-01-01

    Roč. 31, č. 4 (2015), s. 424-437 ISSN 0748-3007 R&D Projects: GA ČR GAP505/12/2467 Grant - others:Marie Curie Felloswhip(CZ) PIOFGA2009-25448 Institutional support: RVO:60077344 Keywords : Hymenoptera * Camponotus * molecular phylogeny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.952, year: 2015 http://onlinelibrary.wiley.com/doi/10.1111/cla.12099/epdf

  7. THE BOLOCAM GALACTIC PLANE SURVEY. X. A COMPLETE SPECTROSCOPIC CATALOG OF DENSE MOLECULAR GAS OBSERVED TOWARD 1.1 mm DUST CONTINUUM SOURCES WITH 7.°5 ≤ l ≤ 194°

    International Nuclear Information System (INIS)

    Shirley, Yancy L.; Svoboda, Brian; Ellsworth-Bowers, Timothy P.; Schlingman, Wayne M.; Ginsburg, Adam; Battersby, Cara; Stringfellow, Guy; Glenn, Jason; Bally, John; Rosolowsky, Erik; Gerner, Thomas; Mairs, Steven; Dunham, Miranda K.

    2013-01-01

    The Bolocam Galactic Plane Survey (BGPS) is a 1.1 mm continuum survey of dense clumps of dust throughout the Galaxy covering 170 deg 2 . We present spectroscopic observations using the Heinrich Hertz Submillimeter Telescope of the dense gas tracers, HCO + and N 2 H + 3-2, for all 6194 sources in the BGPS v1.0.1 catalog between 7.°5 ≤ l ≤ 194°. This is the largest targeted spectroscopic survey of dense molecular gas in the Milky Way to date. We find unique velocities for 3126 (50.5%) of the BGPS v1.0.1 sources observed. Strong N 2 H + 3-2 emission (T mb > 0.5 K) without HCO + 3-2 emission does not occur in this catalog. We characterize the properties of the dense molecular gas emission toward the entire sample. HCO + is very sub-thermally populated and the 3-2 transitions are optically thick toward most BGPS clumps. The median observed line width is 3.3 km s –1 consistent with supersonic turbulence within BGPS clumps. We find strong correlations between dense molecular gas integrated intensities and 1.1 mm peak flux and the gas kinetic temperature derived from previously published NH 3 observations. These intensity correlations are driven by the sensitivity of the 3-2 transitions to excitation conditions rather than by variations in molecular column density or abundance. We identify a subset of 113 sources with stronger N 2 H + than HCO + integrated intensity, but we find no correlations between the N 2 H + /HCO + ratio and 1.1 mm continuum flux density, gas kinetic temperature, or line width. Self-absorbed profiles are rare (1.3%)

  8. THE BOLOCAM GALACTIC PLANE SURVEY. X. A COMPLETE SPECTROSCOPIC CATALOG OF DENSE MOLECULAR GAS OBSERVED TOWARD 1.1 mm DUST CONTINUUM SOURCES WITH 7.°5 ≤ l ≤ 194°

    Energy Technology Data Exchange (ETDEWEB)

    Shirley, Yancy L.; Svoboda, Brian [Steward Observatory, 933 North Cherry Avenue, Tucson, AZ 85721 (United States); Ellsworth-Bowers, Timothy P.; Schlingman, Wayne M.; Ginsburg, Adam; Battersby, Cara; Stringfellow, Guy; Glenn, Jason; Bally, John [CASA, University of Colorado, CB 389, Boulder, CO 80309 (United States); Rosolowsky, Erik [Department of Physics, University of Alberta, 4-181 CCIS Edmonton AB T6G 2E1 (Canada); Gerner, Thomas [Max-Planck-Institut für Astronomie (MPIA), Knigstuhl 17, D-69117 Heidelberg (Germany); Mairs, Steven [Department of Physics and Astronomy, University of Victoria, P.O. Box 3055, STN CSC, Victoria, BC V8W 3P6 (Canada); Dunham, Miranda K. [Department of Astronomy, Yale University, P.O. Box 208101, New Haven, CT 06520 (United States)

    2013-11-01

    The Bolocam Galactic Plane Survey (BGPS) is a 1.1 mm continuum survey of dense clumps of dust throughout the Galaxy covering 170 deg{sup 2}. We present spectroscopic observations using the Heinrich Hertz Submillimeter Telescope of the dense gas tracers, HCO{sup +} and N{sub 2}H{sup +} 3-2, for all 6194 sources in the BGPS v1.0.1 catalog between 7.°5 ≤ l ≤ 194°. This is the largest targeted spectroscopic survey of dense molecular gas in the Milky Way to date. We find unique velocities for 3126 (50.5%) of the BGPS v1.0.1 sources observed. Strong N{sub 2}H{sup +} 3-2 emission (T {sub mb} > 0.5 K) without HCO{sup +} 3-2 emission does not occur in this catalog. We characterize the properties of the dense molecular gas emission toward the entire sample. HCO{sup +} is very sub-thermally populated and the 3-2 transitions are optically thick toward most BGPS clumps. The median observed line width is 3.3 km s{sup –1} consistent with supersonic turbulence within BGPS clumps. We find strong correlations between dense molecular gas integrated intensities and 1.1 mm peak flux and the gas kinetic temperature derived from previously published NH{sub 3} observations. These intensity correlations are driven by the sensitivity of the 3-2 transitions to excitation conditions rather than by variations in molecular column density or abundance. We identify a subset of 113 sources with stronger N{sub 2}H{sup +} than HCO{sup +} integrated intensity, but we find no correlations between the N{sub 2}H{sup +}/HCO{sup +} ratio and 1.1 mm continuum flux density, gas kinetic temperature, or line width. Self-absorbed profiles are rare (1.3%)

  9. Enhancing Management Tools: Molecular Genetic Tracking to Target Microbial Pollution Sources in South Florida Coral Reefs, Year 1 - CRCP project #1114

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Both coastal inlets and treated wastewater outfalls are recognized as major pathways for microbial contaminants from Land-Based Sources of Pollution (LBSP) to enter...

  10. Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

    Science.gov (United States)

    Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

    2018-01-09

    We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

  11. Distributed chemical computing using ChemStar: an open source java remote method invocation architecture applied to large scale molecular data from PubChem.

    Science.gov (United States)

    Karthikeyan, M; Krishnan, S; Pandey, Anil Kumar; Bender, Andreas; Tropsha, Alexander

    2008-04-01

    We present the application of a Java remote method invocation (RMI) based open source architecture to distributed chemical computing. This architecture was previously employed for distributed data harvesting of chemical information from the Internet via the Google application programming interface (API; ChemXtreme). Due to its open source character and its flexibility, the underlying server/client framework can be quickly adopted to virtually every computational task that can be parallelized. Here, we present the server/client communication framework as well as an application to distributed computing of chemical properties on a large scale (currently the size of PubChem; about 18 million compounds), using both the Marvin toolkit as well as the open source JOELib package. As an application, for this set of compounds, the agreement of log P and TPSA between the packages was compared. Outliers were found to be mostly non-druglike compounds and differences could usually be explained by differences in the underlying algorithms. ChemStar is the first open source distributed chemical computing environment built on Java RMI, which is also easily adaptable to user demands due to its "plug-in architecture". The complete source codes as well as calculated properties along with links to PubChem resources are available on the Internet via a graphical user interface at http://moltable.ncl.res.in/chemstar/.

  12. Molecular-beam sampling of a hollow-cathode discharge in argon as a plasma diagnostic and a source for fast neutrals

    International Nuclear Information System (INIS)

    Theuws, P.G.A.; Beijerinck, H.C.W.; Schram, D.C.; Verster, N.F.

    1977-01-01

    Velocity analysis of the molecular beam is done with a time-of-flight method. The measured velocity distribution of the fast neutral atoms is described by the sum of two Maxwell-Boltzmann distributions with temperatures on the order of 0.25 and 1 eV, respectively. This bimodal distribution is attributed to an overpopulation of the high-energy tail of the ion velocity distribution. The measured intensities of the fast neutrals vary between 5 x 10 14 and 7 x 10 15

  13. Campylobacteriosis in urban versus rural areas: a case-case study integrated with molecular typing to validate risk factors and to attribute sources of infection.

    Directory of Open Access Journals (Sweden)

    Simon Lévesque

    Full Text Available Campylobacter infection is a leading cause of bacterial gastroenteritis worldwide, and most clinical cases appear as isolated, sporadic infections for which the source is rarely apparent. From July 2005 to December 2007 we conducted a prospective case-case study of sporadic, domestically-acquired Campylobacter enteritis in rural versus urban areas and a prevalence study of Campylobacter in animal and environmental sources in the Eastern Townships, Quebec. Isolates were typed using Multilocus Sequence Typing (MLST to reinforce the case-case findings and to assign a source probability estimate for each human isolate. The risk of human campylobacteriosis was 1.89-fold higher in rural than urban areas. Unconditional multivariate logistic regression analysis identified two independent risk factors associated with human Campylobacter infections acquired in rural area: occupational exposure to animals (OR = 10.6, 95% CI: 1.2-91, p = 0.032, and household water coming from a private well (OR = 8.3, 95% CI: 3.4-20.4, p<0.0001. A total of 851 C. jejuni isolates (178 human, 257 chicken, 87 bovine, 266 water, 63 wild bird were typed using MLST. Among human isolates, the incidence rates of clonal complexes (CC CC-21, CC-45, and CC-61 were higher in rural than urban areas. MLST-based source attribution analysis indicated that 64.5% of human C. jejuni isolates were attributable to chicken, followed by cattle (25.8%, water (7.4%, and wild birds (2.3%. Chicken was the attributable source for the majority of cases, independent of residential area, sex and age. The increased incidence in rural compared to urban areas was associated with occupational exposure to animals, particularly cattle among those aged 15-34 years, and with consumption of private well water. Both bovine and water exposure appeared to contribute to the seasonal variation in campylobacteriosis. These results provide a basis for developing public education and preventive programs targeting the

  14. The production, molecular weight and viscosifying power of alginate produced by Azotobacter vinelandii is affected by the carbon source in submerged cultures

    Directory of Open Access Journals (Sweden)

    Mauricio A. Trujillo-Roldán

    2015-01-01

    Full Text Available El alginato es un polímero lineal compuesto por ácidos 1,4 manurónico y su epímero, -L- gulurónico y con frecuencia se extrae de algas marinas, como también de bacterias como Azotobacter y Pseudomonas. En este trabajo, se presenta el impacto de diferentes fuentes de carbono convencionales y no convencionales en el crecimiento de A. vinelandii, producción de alginato, su peso molecular promedio (PMP y su capacidad viscosificante. Todos los experimentos se iniciaron con 20 g/L de azúcares totales, donde la más alta concentración de biomasa se obtuvo utilizando suero de leche hidrolizado y desproteinizado (6.67±0.72 g/L, y jugo de caña de azúcar (6.68±0.45 g/L. Sin embargo, la producción máxima de alginato se logró utilizando sacarosa (5.11±0.37 g/L, así como el más alto rendimiento de alginato y productividad específica. Por otra parte, el mayor PMP de alginato se obtuvo con jugo de caña de azúcar (1203±120 kDa. Además, la capacidad viscosificante más alta se obtuvo utilizando suero de leche desproteinizado e hidrolizado (23.8±2.6 cpsL/galg. Esta información sugiere que es posible manipular la productividad y las características moleculares de alginatos como función de la fuente de carbono utilizada. En conjunto con el conocimiento de los efectos de las condiciones ambientales se lograrían altos rendimientos de biopolímeros de alto valor agregado.

  15. Molecular identification of dermatophytosis by polymerase chain reaction (PCR and detection of source of infection by restricted fragment length polymorphism (RFLP

    Directory of Open Access Journals (Sweden)

    BK Jha

    2013-09-01

    Full Text Available Introduction Dermatophytes are responsible for most superficial fungal infections and the estimated lifetime risk of acquiring a dermatophyte infection is between 10-20%. These fungi are mainly classified in three major genera Microsporum, Trichophyton and Epidermophyton. Materials and Methods Clinically suspected 200 cases of dermatophyte infected patients from K. R. Hospital Mysore and Mission Hospital Mysore were included in this descriptive study from January 2011 to June 2012. All the culture positive smear- 10% Potassium Hydroxide (KOH and culture in different dermatophytic medium patients were confirmed by PCR and source of infection was detected (n=10 from PCR positive patients and (n=10 from their domestic animals by PCR-RFLP methods targeting 18S rDNA regions of fungi. Results Out of 200 clinically suspected cases KOH mount was positive in 143 (71.5% cases and culture was positive in 132(66% cases. The isolates belonged to three genera and eight species as T.mentagrophytes 52(39.4%, T.rubrum 30(22.7%, T.violacium 18(13.6%, T.verrucosum 11(8.3%, E.floccosum 10(7.6%, M.canis 6(4.5%, T.tonsurans 03(2.3% and T.schollenii 2(1.5%. To identify the source of infection 10 animals ,one each from the houses of 10 patients who were PCR positive were also subjected to PCR and RFLP. The animals and the patients were found to be infected by same organisms T.verrucosum .This indicates that T.verrucosum infection is from animal source. Conclusion Dermatophytic infections are more common infectious disease. Preliminary diagnosis of dermatophytosis can be done by KOH mount and culture, which takes longer time to report and cannot differentiate at the genus and species level. Results indicate that PCR-RFLP may be considered as gold standard for the diagnosis and confirmation of source of infection of dermatophytosis and can aid the clinician in initiating prompt and appropriate antifungal therapy. Journal of College of Medical Sciences-Nepal, 2012, Vol-8

  16. Molecular inference of sources and spreading patterns of Plasmodium falciparum malaria parasites in internally displaced persons settlements in Myanmar-China border area.

    Science.gov (United States)

    Lo, Eugenia; Zhou, Guofa; Oo, Winny; Lee, Ming-Chieh; Baum, Elisabeth; Felgner, Philip L; Yang, Zhaoqing; Cui, Liwang; Yan, Guiyun

    2015-07-01

    In Myanmar, civil unrest and establishment of internally displaced persons (IDP) settlement along the Myanmar-China border have impacted malaria transmission. The growing IDP populations raise deep concerns about health impact on local communities. Microsatellite markers were used to examine the source and spreading patterns of Plasmodium falciparum between IDP settlement and surrounding villages in Myanmar along the China border. Genotypic structure of P. falciparum was compared over the past three years from the same area and the demographic history was inferred to determine the source of recent infections. In addition, we examined if border migration is a factor of P. falciparum infections in China by determining gene flow patterns across borders. Compared to local community, the IDP samples showed a reduced and consistently lower genetic diversity over the past three years. A strong signature of genetic bottleneck was detected in the IDP samples. P. falciparum infections from the border regions in China were genetically similar to Myanmar and parasite gene flow was not constrained by geographical distance. Reduced genetic diversity of P. falciparum suggested intense malaria control within the IDP settlement. Human movement was a key factor to the spread of malaria both locally in Myanmar and across the international border. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Saccharide Composition in Fine and Coarse Particulate Matter and Soils in Central Arizona and Use of Saccharides as Molecular Markers for Source Apportionment

    Science.gov (United States)

    Jia, Y.; Clements, A.; Fraser, M.

    2009-04-01

    The desert southwestern United States routinely exceeds health-based standards for coarse particulate matter [1]. PM10 concentrations are high in both urban and rural areas and are believed to originate from fugitive dust emissions from agricultural fields and roads and soil erosion from the surrounding desert locations. Soil together with its associated biota contains a complex mixture of biogenic detritus, including plant detritus, airborne microbes comprised of bacteria, viruses, spores of lichens and fungi, small algae, and protozoan cysts [4][5], which can mostly become airborne when winds are strong enough and soil dry enough to be re-entrained into the atmosphere [3]. Other potential sources to PM10 may include primary biological aerosol particles (PBAPs), given a multitude of flower, grass, and fungal species that thrive in the Sonoran desert and actively release pollens and spores throughout the year [2]. However, because soil and fugitive dust is also believed to contain a large number of these biological particles and is considered as a secondary host of PBAPs [3] [4], the role and contribution of PBAPs as a direct ambient PM source in the desert southwest have not been clearly stated or investigated. In an effort to identify and assess the relative contribution of these and other major PM sources in the southwestern US region, and particularly to assess the contribution from soil and fugitive dust, a series of ambient PM samples and soil samples were collected in Higley, AZ, USA, a suburb of the Phoenix metropolitan area which has seen rapid urban sprawl onto agricultural lands. Because of their suggested ability to track biologically important organic materials from natural environment [4][6][7][8][9][10], saccharides were chosen as the key compounds to trace the release of soil dusts into the atmosphere, and to elucidate other major sources that contribute to the PM levels in this location in the arid southwestern US. To this end, saccharide compounds

  18. Ion sources for accelerators

    International Nuclear Information System (INIS)

    Alton, G.D.

    1974-01-01

    A limited review of low charge sate positive and negative ion sources suitable for accelerator use is given. A brief discussion is also given of the concepts underlying the formation and extraction of ion beams. Particular emphasis is placed on the technology of ion sources which use solid elemental or molecular compounds to produce vapor for the ionization process

  19. Unique low-molecular-weight lignin with high purity extracted from wood by deep eutectic solvents (DES): a source of lignin for valorization

    Energy Technology Data Exchange (ETDEWEB)

    Alvarez-Vasco, Carlos; Ma, Ruoshui; Quintero, Melissa; Guo, Mond; Geleynse, Scott; Ramasamy, Karthikeyan K.; Wolcott, Michael; Zhang, Xiao

    2016-01-01

    This paper reports a new method of applying Deep Eutectic Solvents (DES) for extracting lignin from woody biomass with high yield and high purity. DES mixtures prepared from Choline Chloride (ChCl) and four hydrogen-bond donors–acetic acid, lactic acid, levulinic acid and glycerol–were evaluated for treatment of hardwood (poplar) and softwood (D. fir). It was found that these DES treatments can selectively extract a significant amount of lignin from wood with high yields: 78% from poplar and 58% from D. fir. The extracted lignin has high purity (95%) with unique structural properties. We discover that DES can selectively cleave ether linkages in wood lignin and facilitate lignin removal from wood. The mechanism of DES cleavage of ether bonds between phenylpropane units was investigated. The results from this study demonstrate that DES is a promising solvent for wood delignification and the production of a new source of lignin with promising potential applications.

  20. Identification of abiotic and biotic reductive dechlorination in a chlorinated ethene plume after thermal source remediation by means of isotopic and molecular biology tools

    DEFF Research Database (Denmark)

    Badin, Alice; Broholm, Mette Martina; Jacobsen, Carsten S.

    2016-01-01

    Thermal tetrachloroethene (PCE) remediation by steam injection in a sandy aquifer led to the release of dissolved organic carbon (DOC) from aquifer sediments resulting in more reduced redox conditions, accelerated PCE biodegradation, and changes in microbial populations. These changes were...... documented by comparing data collected prior to the remediation event and eight years later. Based on the premise that dual C-Cl isotope slopes reflect ongoing degradation pathways, the slopes associated with PCE and TCE suggest the predominance of biotic reductive dechlorination near the source area. PCE...... is supported by the relative lack of Dhc in the downgradient part of the plume. The results of this study show that thermal remediation can enhance the biodegradation of chlorinated ethenes, and that this effect can be traced to the mobilisation of DOC due to steam injection. This, in turn, results in more...

  1. An Ocean Basin of Dirt? Using Molecular Biomarkers and Radiocarbon to Identify Organic Carbon Sources and their Preservation in the Arctic Ocean

    Science.gov (United States)

    Harvey, H.; Belicka, L. L.

    2005-12-01

    In the modern Arctic Ocean, primary production in waters over the broad continental shelves and under ice contributes an estimated 250 Mt/yr of POC to Arctic waters. The delivery of terrestrial material from large rivers, ice transport and through coastal erosion adds at least an additional 12 Mt/yr of POC. Although the marine organic carbon signal in Arctic Ocean exceeds that of terrestrial carbon by an order or magnitude or more, recent evidence suggests that this balance is not maintained and significant fractions of terrestrial carbon is preserved in sediments. Using an integrated approach combining lipid biomarkers and radiocarbon dating in particles and sediments, the process of organic carbon recycling and historical changes in its sources and preservation has been examined. A suite of lipid biomarkers in particles and sediments of western Arctic shelves and basins were measured and principle components analysis (PCA) used to allow a robust comparison among the 120+ individual compounds to assign organic sources and relative inputs. Offshore particles from the chlorophyll maximum contained abundant algal markers (e.g. 20:5 and 22:6 FAMEs), low concentrations of terrestrial markers (amyrins and 24-ethylcholest-5-en-3b-ol), and reflected modern 14C values. Particles present in deeper halocline waters also reflect marine production, but a portion of older, terrestrial carbon accompanies the sinking of the spring bloom. Surface and deeper sediments of basins contain older organic carbon and low concentrations of algal biomarkers, suggesting that marine carbon produced in surface waters is rapidly recycled. Taken together, these observations suggest that marine derived organic matter produced in shallow waters fuels carbon cycling, but relatively small amounts are preserved in sediments. As a result, the organic carbon preserved in sediments contrasts sharply to that typically observed in lower latitudes, with an increasing terrestrial signature with distance

  2. Effect of disrupted mitochondria as a source of damage-associated molecular patterns on the production of tumor necrosis factor α by splenocytes from dogs.

    Science.gov (United States)

    Friedenberg, Steven G; Strange, Heather R; Guillaumin, Julien; VanGundy, Zachary C; Crouser, Elliott D; Papenfuss, Tracey L

    2016-06-01

    OBJECTIVE To evaluate the effects of damage-associated molecular patterns (DAMPs) derived from disrupted mitochondria on canine splenocytes and other immune cells. SAMPLES Liver, spleen, and bone marrow samples obtained from 8 cadavers of healthy research Beagles that had been euthanized for other purposes. PROCEDURES Mitochondria were obtained from canine hepatocytes, and mitochondrial DAMPs (containing approx 75% mitochondrial proteins) were prepared. Mitochondrial DAMPs and the nuclear cytokine high-mobility group box protein 1 were applied to splenocytes, bone marrow-differentiated dendritic cells, and a canine myelomonocytic cell (DH82) line for 6 or 24 hours. Cell culture supernatants from splenocytes, dendritic cells, and DH82 cells were assayed for tumor necrosis factor α with an ELISA. Expression of tumor necrosis factor α mRNA in splenocytes was evaluated with a quantitative real-time PCR assay. RESULTS In all cell populations evaluated, production of tumor necrosis factor α was consistently increased by mitochondrial DAMPs at 6 hours (as measured by an ELISA). In contrast, high-mobility group box protein 1 did not have any independent proinflammatory effects in this experimental system. CONCLUSIONS AND CLINICAL RELEVANCE The study revealed an in vitro inflammatory effect of mitochondrial DAMPs (containing approx 75% mitochondrial proteins) in canine cells and validated the use of an in vitro splenocyte model to assess DAMP-induced inflammation in dogs. This experimental system may aid in understanding the contribution of DAMPs to sepsis and the systemic inflammatory response syndrome in humans. Further studies in dogs are needed to validate the biological importance of these findings and to evaluate the in vivo role of mitochondrial DAMPs in triggering and perpetuating systemic inflammatory states.

  3. The formation of hexagonal-shaped InGaN-nanodisk on GaN-nanowire observed in plasma source molecular beam epitaxy

    KAUST Repository

    Ng, Tien Khee

    2014-03-08

    We report on the properties and growth kinetics of defect-free, photoluminescence (PL) efficient mushroom-like nanowires (MNWs) in the form of ~30nm thick hexagonal-shaped InGaN-nanodisk on GaN nanowires, coexisting with the conventional rod-like InGaN-on-GaN nanowires (RNWs) on (111)-silicon-substrate. When characterized using confocal microscopy (CFM) with 458nm laser excitation, while measuring spontaneous-emission at fixed detection wavelengths, the spatial intensity map evolved from having uniform pixelated emission, to having only an emission ring, and then a round emission spot. This corresponds to the PL emission with increasing indium composition; starting from emission mainly from the RNW, and then the 540 nm emission from one MNWs ensemble, followed by the 590 nm emission from a different MNW ensemble, respectively. These hexagonal-shaped InGaN-nano-disks ensembles were obtained during molecular-beam-epitaxy (MBE) growth. On the other hand, the regular rod-like InGaN-on-GaN nanowires (RNWs) were emitting at a shorter peak wavelength of 490 nm. While the formation of InGaN rod-like nanowire is well-understood, the formation of the hexagonal-shaped InGaN-nanodisk-on-GaN-nanowire requires further investigation. It was postulated to arise from the highly sensitive growth kinetics during plasma-assisted MBE of InGaN at low temperature, i.e. when the substrate temperature was reduced from 800 °C (GaN growth) to <600 °C (InGaN growth), during which sparsely populated metal-droplet formation prevails and further accumulated more indium adatoms due to a higher cohesive bond between metallic molecules. © (2014) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

  4. Molecular beam epitaxy of InP single junction and InP/In0.53Ga0.47As monolithically integrated tandem solar cells using solid phosphorous source material

    International Nuclear Information System (INIS)

    Delaney, A.; Chin, K.; Street, S.; Newman, F.; Aguilar, L.; Ignatiev, A.; Monier, C.; Velela, M.; Freundlich, A.

    1998-01-01

    This work reports the first InP solar cells, InP/In 0.53 Ga 0.47 As tandem solar cells and InP tunnel junctions to be grown using a solid phosphorous source cracker cell in a molecular beam epitaxy system. High p-type doping achieved with this system allowed for the development of InP tunnel junctions. These junctions which allow for improved current matching in subsequent monolithically integrated tandem devices also do not absorb photons which can be utilized in the InGaAs structure. Photocurrent spectral responses compared favorably to devices previously grown in a chemical beam epitaxy system. High resolution x-ray scans demonstrated good lattice matching between constituent parts of the tandem cell. AM0 efficiencies of both InP and InP/InGaAs tandem cells are reported

  5. High-quality AlGaN/GaN grown on sapphire by gas-source molecular beam epitaxy using a thin low-temperature AlN layer

    Energy Technology Data Exchange (ETDEWEB)

    Jurkovic, M.J.; Li, L.K.; Turk, B.; Wang, W.I.; Syed, S.; Simonian, D.; Stormer, H.L.

    2000-07-01

    Growth of high-quality AlGaN/GaN heterostructures on sapphire by ammonia gas-source molecular beam epitaxy is reported. Incorporation of a thin AlN layer grown at low temperature within the GaN buffer is shown to result in enhanced electrical and structural characteristics for subsequently grown heterostructures. AlGaN/GaN structures exhibiting reduced background doping and enhanced Hall mobilities (2100, 10310 and 12200 cm{sup 2}/Vs with carrier sheet densities of 6.1 x 10{sup 12} cm{sup {minus}2}, and 5.8 x 10{sup 12} cm{sup {minus}2} at 300 K, 77 K, and 0.3 K, respectively) correlate with dislocation filtering in the thin AlN layer. Magnetotransport measurements at 0.3 K reveal well-resolved Shubnikov-de Haas oscillations starting at 3 T.

  6. High-efficiency silicon doping of InP and In0.53Ga0.47As in gas source and metalorganic molecular beam epitaxy using silicon tetrabromide

    International Nuclear Information System (INIS)

    Jackson, S.L.; Fresina, M.T.; Baker, J.E.; Stillman, G.E.

    1994-01-01

    Efficient vapor source Si doping of InP and In 0.53 Ga 0.47 As have been demonstrated using SiBr 4 as the Si source for both gas source (GSMBE) and metalorganic molecular beam epitaxy (MOMBE). Net electron concentrations ranging from n=2x10 17 to 6.8x10 19 cm -3 and from 9x10 16 to 3x10 19 cm -3 have been obtained for InP and In 0.53 Ga 0.47 As, respectively. Comparison of these data with those for Si 2 H 6 indicate that the Si incorporation efficiency with SiBr 4 is more than 10 000 times greater than with Si 2 H 6 for substrate temperatures in the range of 475≤T s ≤500 degree C. Specular surface morphologies were obtained, even for the most heavily doped samples. While [Si] as high as 1.8x10 20 cm -3 was obtained in InP, the net electron concentrations and 300 K Hall mobilities decrease with increasing [Si] for [Si]>6.8x10 19 cm -3 . Contact resistances as low as R c =3x10 -8 Ω cm 2 were obtained using a nonalloyed Ti/Pt/Au contact to InP layers doped to n=6.3x10 19 cm -3 . During GSMBE growth, an increased Si background concentration ([Si]∼2x10 17 cm -3 ) was observed after extended use of the SiBr 4 source for these heavy doping concentrations. This increased background was not observed in MOMBE-grown material. Depth profiles of pulse-doped structures indicate the absence of memory effects for structures grown by MOMBE

  7. High power and spectral purity continuous-wave photonic THz source tunable from 1 to 4.5 THz for nonlinear molecular spectroscopy

    Science.gov (United States)

    Kiessling, J.; Breunig, I.; Schunemann, P. G.; Buse, K.; Vodopyanov, K. L.

    2013-10-01

    We report a diffraction-limited photonic terahertz (THz) source with linewidth OP) gallium arsenide (GaAs) via intracavity frequency mixing between the two closely spaced resonating signal and idler waves of an optical parametric oscillator (OPO) operating near λ = 2 μm. The doubly resonant type II OPO is based on a periodically poled lithium niobate (PPLN) pumped by a single-frequency Yb:YAG disc laser at 1030 nm. We take advantage of the enhancement of both optical fields inside a high-finesse OPO cavity: with 10 W of 1030 nm pump, 100 W of intracavity power near 2 μm was attained with GaAs inside cavity. This allows dramatic improvement in terms of generated THz power, as compared to the state-of-the art CW methods. We achieved >25 μW of single-frequency tunable CW THz output power scalable to >1 mW with proper choice of pump laser wavelength.

  8. Molecular distribution, seasonal variation, chemical transformation and sources of dicarboxylic acids and related compounds in atmospheric aerosols at remote marine Gosan site, Jeju Island

    Science.gov (United States)

    Kundu, S.; Kawamura, K.; Lee, M.

    2009-12-01

    between Chinese cities and Chichi-jima Island in Japan was observed higher than those in Chinese cities and lower than that of the Chichi-jima Island, pointing to the formation of diacid during long range transport. The lowest values of adipic/azelaic (C6/C9) and phthalic/azelaic (Ph/C9) were observed as a result of the overwhelming biogenic emission of the precursors (e.g., unsaturated fatty acids) of azelaic acid in summer.In this study, we will also discuss the sources and transport pathways of diacids and related compounds resolved using a hybrid receptor model, potential source contribution function (PSCF) and model results will be compared with available in-situ observations in East Asia.

  9. Crossed molecular beams

    International Nuclear Information System (INIS)

    Lee, Y.T.

    1976-01-01

    Research activities with crossed molecular beams at Lawrence Berkeley Laboratory during 1976 are described. Topics covered include: scattering of Ar*, Kr*, with Xe; metastable rare gas interactions, He* + H 2 ; an atomic and molecular halogen beam source; a crossed molecular beam study of the Cl + Br 2 → BrCl + Br reaction; O( 3 P) reaction dynamics, development of the high pressure plasma beam source; energy randomization in the Cl + C 2 H 3 Br → Br + C 2 H 3 Cl reaction; high resolution photoionization studies of NO and ICl; photoionization of (H 2 O)/sub n/ and (NH 3 ) 2 ; photoionization mass spectroscopy of NH 3 + and O 3 + ; photo fragmentation of bromine; and construction of chemiluminescence-laser fluorescence crossed molecular beam machine

  10. Anopheles (Kerteszia cruzii (DIPTERA: CULICIDAE IN PERIDOMICILIARY AREA DURING ASYMPTOMATIC MALARIA TRANSMISSION IN THE ATLANTIC FOREST: MOLECULAR IDENTIFICATION OF BLOOD-MEAL SOURCES INDICATES HUMANS AS PRIMARY INTERMEDIATE HOSTS

    Directory of Open Access Journals (Sweden)

    Karin Kirchgatter

    2014-09-01

    Full Text Available Anopheles (Kerteszia cruzii has been implicated as the primary vector of human and simian malarias out of the Brazilian Amazon and specifically in the Atlantic Forest regions. The presence of asymptomatic human cases, parasite-positive wild monkeys and the similarity between the parasites infecting them support the discussion whether these infections can be considered as a zoonosis. Although many aspects of the biology of An. cruzii have already been addressed, studies conducted during outbreaks of malaria transmission, aiming at the analysis of blood feeding and infectivity, are missing in the Atlantic Forest. This study was conducted in the location of Palestina, Juquitiba, where annually the majority of autochthonous human cases are notified in the Atlantic Forest of the state of São Paulo. Peridomiciliary sites were selected for collection of mosquitoes in a perimeter of up to 100 m around the residences of human malaria cases. The mosquitoes were analyzed with the purpose of molecular identification of blood-meal sources and to examine the prevalence of Plasmodium. A total of 13,441 females of An. (Ker. cruzii were collected. The minimum infection rate was calculated at 0.03% and 0.01%, respectively, for P. vivax and P. malariae and only human blood was detected in the blood-fed mosquitoes analyzed. This data reinforce the hypothesis that asymptomatic human carriers are the main source of anopheline infection in the peridomiciliary area, making the probability of zoonotic transmission less likely to happen.

  11. Anopheles (Kerteszia) cruzii (Diptera: Culicidae) in peridomiciliary area during asymptomatic malaria transmission in the Atlantic Forest: molecular identification of blood-meal sources indicates humans as primary intermediate hosts.

    Science.gov (United States)

    Kirchgatter, Karin; Tubaki, Rosa Maria; Malafronte, Rosely dos Santos; Alves, Isabel Cristina; Lima, Giselle Fernandes Maciel de Castro; Guimarães, Lilian de Oliveira; Zampaulo, Robson de Almeida; Wunderlich, Gerhard

    2014-01-01

    Anopheles (Kerteszia) cruzii has been implicated as the primary vector of human and simian malarias out of the Brazilian Amazon and specifically in the Atlantic Forest regions. The presence of asymptomatic human cases, parasite-positive wild monkeys and the similarity between the parasites infecting them support the discussion whether these infections can be considered as a zoonosis. Although many aspects of the biology of An. cruzii have already been addressed, studies conducted during outbreaks of malaria transmission, aiming at the analysis of blood feeding and infectivity, are missing in the Atlantic Forest. This study was conducted in the location of Palestina, Juquitiba, where annually the majority of autochthonous human cases are notified in the Atlantic Forest of the state of São Paulo. Peridomiciliary sites were selected for collection of mosquitoes in a perimeter of up to 100 m around the residences of human malaria cases. The mosquitoes were analyzed with the purpose of molecular identification of blood-meal sources and to examine the prevalence of Plasmodium. A total of 13,441 females of An. (Ker.) cruzii were collected. The minimum infection rate was calculated at 0.03% and 0.01%, respectively, for P. vivax and P. malariae and only human blood was detected in the blood-fed mosquitoes analyzed. This data reinforce the hypothesis that asymptomatic human carriers are the main source of anopheline infection in the peridomiciliary area, making the probability of zoonotic transmission less likely to happen.

  12. Molecular sources of residual cardiovascular risk, clinical signals, and innovative solutions: relationship with subclinical disease, undertreatment, and poor adherence: implications of new evidence upon optimizing cardiovascular patient outcomes

    Directory of Open Access Journals (Sweden)

    Kones R

    2013-10-01

    Full Text Available Richard KonesCardiometabolic Research Institute, Houston, TX, USAAbstract: Residual risk, the ongoing appreciable risk of major cardiovascular events (MCVE in statin-treated patients who have achieved evidence-based lipid goals, remains a concern among cardiologists. Factors that contribute to this continuing risk are atherogenic non-low-density lipoprotein (LDL particles and atherogenic processes unrelated to LDL cholesterol, including other risk factors, the inherent properties of statin drugs, and patient characteristics, ie, genetics and behaviors. In addition, providers, health care systems, the community, public policies, and the environment play a role. Major statin studies suggest an average 28% reduction in LDL cholesterol and a 31% reduction in relative risk, leaving a residual risk of about 69%. Incomplete reductions in risk, and failure to improve conditions that create risk, may result in ongoing progression of atherosclerosis, with new and recurring lesions in original and distant culprit sites, remodeling, arrhythmias, rehospitalizations, invasive procedures, and terminal disability. As a result, identification of additional agents to reduce residual risk, particularly administered together with statin drugs, has been an ongoing quest. The current model of atherosclerosis involves many steps during which disease may progress independently of guideline-defined elevations in LDL cholesterol. Differences in genetic responsiveness to statin therapy, differences in ability of the endothelium to regenerate and repair, and differences in susceptibility to nonlipid risk factors, such as tobacco smoking, hypertension, and molecular changes associated with obesity and diabetes, may all create residual risk. A large number of inflammatory and metabolic processes may also provide eventual therapeutic targets to lower residual risk. Classically, epidemiologic and other evidence suggested that raising high-density lipoprotein (HDL cholesterol

  13. Magnetismo Molecular (Molecular Magentism)

    Energy Technology Data Exchange (ETDEWEB)

    Reis, Mario S [Universidade Federal Fluminense, Brasil; Moreira Dos Santos, Antonio F [ORNL

    2010-07-01

    The new synthesis processes in chemistry open a new world of research, new and surprising materials never before found in nature can now be synthesized and, as a wonderful result, observed a series of physical phenomena never before imagined. Among these are many new materials the molecular magnets, the subject of this book and magnetic properties that are often reflections of the quantum behavior of these materials. Aside from the wonderful experience of exploring something new, the theoretical models that describe the behavior these magnetic materials are, in most cases, soluble analytically, which allows us to know in detail the physical mechanisms governing these materials. Still, the academic interest in parallel this subject, these materials have a number of properties that are promising to be used in technological devices, such as in computers quantum magnetic recording, magnetocaloric effect, spintronics and many other devices. This volume will journey through the world of molecular magnets, from the structural description of these materials to state of the art research.

  14. Molecular hematology

    National Research Council Canada - National Science Library

    Provan, Drew; Gribben, John

    2010-01-01

    ... The molecular basis of hemophilia, 219 Paul LF Giangrande 4 The genetics of acute myeloid leukemias, 42 Carolyn J Owen & Jude Fitzgibbon 19 The molecular basis of von Willebrand disease, 233 Luciano Baronc...

  15. Computational Chemistry and Reaction Engineering Workbench

    Energy Technology Data Exchange (ETDEWEB)

    J. Thomas Mckinnon

    2003-12-19

    The chemical process industries are among the most energy intensive in the US. While much of the energy use cannot be avoided, (e.g., feedstock energy or separations costs), there are tremendous gains to be had through simulation-based optimizations. The heart of any chemical operation is the chemical reactor and it is here that gains can be made either directly (e.g., reduced heat flux) or indirectly (e.g., reduced downstream separations cost due to more efficient reactor design). The objective of this project was to develop an integrated suite of software to facilitate the simulation and optimization of chemical reactors. In the phase of the project supported by this grant, we focused specifically on gas-phase chemical processes such as combustion and pyrolysis.

  16. Workbench surface editor of brain cortical surface

    Science.gov (United States)

    Dow, Douglas E.; Nowinski, Wieslaw L.; Serra, Luis

    1996-04-01

    We have developed a 3D reach-in tool to manually reconstruct 3D cortical surface patches from 2D brain atlas images. The first application of our cortex editor is building 3D functional maps, specifically Brodmann's areas. This tool may also be useful in clinical practice to adjust incorrectly mapped atlas regions due to the deforming effect of lesions. The cortex editor allows a domain expert to control the correlation of control points across slices. Correct correlation has been difficult for 3D reconstruction algorithms because the atlas slices are far apart and because of the complex topology of the cortex which differs so much from slice to slice. Also, higher precision of the resulting surfaces is demanded since these define 3D brain atlas features upon which future stereotactic surgery may be based. The cortex editor described in this paper provides a tool suitable for a domain expert to use in defining the 3D surface of a Brodmann's area.

  17. System of Systems Analytic Workbench - 2017

    Science.gov (United States)

    2017-08-31

    Genetic Algorithm and Particle Swarm Optimization with Type-2 Fuzzy Sets for Generating Systems of Systems Architectures. Procedia Computer Science...The application effort involves modeling an existing messaging network to perform real-time situational awareness. The Analytical Workbench’s

  18. Enhancement of Two-Dimensional Electron-Gas Properties by Zn Polar ZnMgO/MgO/ZnO Structure Grown by Radical-Source Laser Molecular Beam Epitaxy

    Directory of Open Access Journals (Sweden)

    Li Meng

    2015-01-01

    Full Text Available A Zn polar ZnMgO/MgO/ZnO structure with low Mg composition Zn1-xMgxO layer (x = 0.05 grown on a-plane (11–20 sapphire by radical-source laser molecular beam epitaxy was reported. The insertion of a thin (1 nm MgO layer between ZnMgO and ZnO layers in the ZnMgO/ZnO 2DEG structures results in an increase of 2DEG sheet density and affects electron mobility slightly. The carrier concentration reached a value as high as 1.1 × 1013 cm−2, which was confirmed by C-V measurements. A high Hall mobility of 3090 cm2/Vs at 10 K and 332 cm2/Vs at RT was observed from Zn0.95Mg0.05O/MgO/ZnO heterostructure. The choice of the thickness of MgO was discussed. The dependence of carrier sheet density of 2DEG on ZnMgO layer thickness was calculated in theory and the theoretical prediction and experimental results agreed well.

  19. Molecular ion photofragment spectroscopy

    International Nuclear Information System (INIS)

    Bustamente, S.W.

    1983-11-01

    A new molecular ion photofragment spectrometer is described which features a supersonic molecular beam ion source and a radio frequency octapole ion trap interaction region. This unique combination allows several techniques to be applied to the problem of detecting a photon absorption event of a molecular ion. In particular, it may be possible to obtain low resolution survey spectra of exotic molecular ions by using a direct vibrational predissociation process, or by using other more indirect detection methods. The use of the spectrometer is demonstrated by measuring the lifetime of the O 2 + ( 4 π/sub u/) metastable state which is found to consist of two main components: the 4 π/sub 5/2/ and 4 π/sub -1/2/ spin components having a long lifetime (approx. 129 ms) and the 4 π/sub 3/2/ and 4 π/sub 1/2/ spin components having a short lifetime (approx. 6 ms)

  20. Method development for the determination of fluorine in toothpaste via molecular absorption of aluminum mono fluoride using a high-resolution continuum source nitrous oxide/acetylene flame atomic absorption spectrophotometer.

    Science.gov (United States)

    Ozbek, Nil; Akman, Suleyman

    2012-05-30

    Fluorine was determined via the rotational molecular absorption line of aluminum mono fluoride (AlF) generated in C(2)H(2)/N(2)O flame at 227.4613 nm using a high-resolution continuum source flame atomic absorption spectrophotometer (HR-CS-FAAS). The effects of AlF wavelength, burner height, fuel rate (C(2)H(2)/N(2)O) and amount of Al on the accuracy, precision and sensitivity were investigated and optimized. The Al-F absorption band at 227.4613 nm was found to be the most suitable analytical line with respect to sensitivity and spectral interferences. Maximum sensitivity and a good linearity were obtained in acetylene-nitrous oxide flame at a flow rate of 210 L h(-1) and a burner height of 8mm using 3000 mg L(-1) of Al for 10-1000 mg L(-1)of F. The accuracy and precision of the method were tested by analyzing spiked samples and waste water certified reference material. The results were in good agreement with the certified and spiked amounts as well as the precision of several days during this study was satisfactory (RSD<10%). The limit of detection and characteristic concentration of the method were 5.5 mg L(-1) and 72.8 mg L(-1), respectively. Finally, the fluorine concentrations in several toothpaste samples were determined. The results found and given by the producers were not significantly different. The method was simple, fast, accurate and sensitive. Copyright © 2012 Elsevier B.V. All rights reserved.

  1. Substructured multibody molecular dynamics.

    Energy Technology Data Exchange (ETDEWEB)

    Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B. (Johns Hopkins University, Baltimore, MD); Lehoucq, Richard B.; Crozier, Paul Stewart; Ismail, Ahmed E.; Mukherjee, Rudranarayan M. (Rensselaer Polytechnic Institute, Troy, NY); Draganescu, Andrei I.

    2006-11-01

    We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

  2. RF Wave Simulation Using the MFEM Open Source FEM Package

    Science.gov (United States)

    Stillerman, J.; Shiraiwa, S.; Bonoli, P. T.; Wright, J. C.; Green, D. L.; Kolev, T.

    2016-10-01

    A new plasma wave simulation environment based on the finite element method is presented. MFEM, a scalable open-source FEM library, is used as the basis for this capability. MFEM allows for assembling an FEM matrix of arbitrarily high order in a parallel computing environment. A 3D frequency domain RF physics layer was implemented using a python wrapper for MFEM and a cold collisional plasma model was ported. This physics layer allows for defining the plasma RF wave simulation model without user knowledge of the FEM weak-form formulation. A graphical user interface is built on πScope, a python-based scientific workbench, such that a user can build a model definition file interactively. Benchmark cases have been ported to this new environment, with results being consistent with those obtained using COMSOL multiphysics, GENRAY, and TORIC/TORLH spectral solvers. This work is a first step in bringing to bear the sophisticated computational tool suite that MFEM provides (e.g., adaptive mesh refinement, solver suite, element types) to the linear plasma-wave interaction problem, and within more complicated integrated workflows, such as coupling with core spectral solver, or incorporating additional physics such as an RF sheath potential model or kinetic effects. USDoE Awards DE-FC02-99ER54512, DE-FC02-01ER54648.

  3. Molecular Diagnostics

    OpenAIRE

    Choe, Hyonmin; Deirmengian, Carl A.; Hickok, Noreen J.; Morrison, Tiffany N.; Tuan, Rocky S.

    2015-01-01

    Orthopaedic infections are complex conditions that require immediate diagnosis and accurate identification of the causative organisms to facilitate appropriate management. Conventional methodologies for diagnosis of these infections sometimes lack accuracy or sufficient rapidity. Current molecular diagnostics are an emerging area of bench-to-bedside research in orthopaedic infections. Examples of promising molecular diagnostics include measurement of a specific biomarker in the synovial fluid...

  4. Molecular genetics

    International Nuclear Information System (INIS)

    Parkinson, D.R.; Krontiris, T.G.

    1986-01-01

    In this chapter the authors review new findings concerning the molecular genetics of malignant melanoma in the context of other information obtained from clinical, epidemiologic, and cytogenetic studies in this malignancy. These new molecular approaches promise to provide a more complete understanding of the mechanisms involved in the development of melanoma, thereby suggesting new methods for its treatment and prevention

  5. Molecular Modeling

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 9; Issue 5. Molecular Modeling: A Powerful Tool for Drug Design and Molecular Docking. Rama Rao Nadendla. General Article Volume 9 Issue 5 May 2004 pp 51-60. Fulltext. Click here to view fulltext PDF. Permanent link:

  6. Compact ion accelerator source

    Science.gov (United States)

    Schenkel, Thomas; Persaud, Arun; Kapadia, Rehan; Javey, Ali

    2014-04-29

    An ion source includes a conductive substrate, the substrate including a plurality of conductive nanostructures with free-standing tips formed on the substrate. A conductive catalytic coating is formed on the nanostructures and substrate for dissociation of a molecular species into an atomic species, the molecular species being brought in contact with the catalytic coating. A target electrode placed apart from the substrate, the target electrode being biased relative to the substrate with a first bias voltage to ionize the atomic species in proximity to the free-standing tips and attract the ionized atomic species from the substrate in the direction of the target electrode.

  7. Molecular geometry

    CERN Document Server

    Rodger, Alison

    1995-01-01

    Molecular Geometry discusses topics relevant to the arrangement of atoms. The book is comprised of seven chapters that tackle several areas of molecular geometry. Chapter 1 reviews the definition and determination of molecular geometry, while Chapter 2 discusses the unified view of stereochemistry and stereochemical changes. Chapter 3 covers the geometry of molecules of second row atoms, and Chapter 4 deals with the main group elements beyond the second row. The book also talks about the complexes of transition metals and f-block elements, and then covers the organometallic compounds and trans

  8. Sources And Compositional Distribution Of Polycyclic Aromatic ...

    African Journals Online (AJOL)

    For molecular mass 178, an anthracene to anthracene plus phenanthrene ratio ≤ 0.10 was taken as indication of petroleum related sources, while a ratio > 0.10 indicated dominance of combustion related sources. For molecular mass 202, a fluoranthene to fluoranthene plus pyrene ratio ≤ 0.50 was indication of petroleum ...

  9. Molecular Electronics

    DEFF Research Database (Denmark)

    Jennum, Karsten Stein

    This thesis includes the synthesis and characterisation of organic compounds designed for molecular electronics. The synthesised organic molecules are mainly based on two motifs, the obigo(phenyleneethynylenes) (OPE)s and tetrathiafulvalene (TTF) as shown below. These two scaffolds (OPE and TTF......) are chemically merged together to form cruciform-like structures that are an essential part of the thesis. The cruciform molecules were subjected to molecular conductance measurements to explore their capability towards single-crystal field-effect transistors (Part 1), molecular wires, and single electron......, however, was obtained by a study of a single molecular transistor. The investigated OPE5-TTF compound was captured in a three-terminal experiment, whereby manipulation of the molecule’s electronic spin was possible in different charge states. Thus, we demonstrated how the cruciform molecules could...

  10. Molecular sciences

    International Nuclear Information System (INIS)

    Anon.

    1975-01-01

    The research in molecular sciences summarized includes photochemistry, radiation chemistry, geophysics, electromechanics, heavy-element oxidizers , heavy element chemistry collisions, atoms, organic solids. A list of publications is included

  11. Tuned sources of submillimetre radiation

    International Nuclear Information System (INIS)

    Berezhnyj, V.L.

    1981-01-01

    The main present directions of development of sources of frequency coherent tuned radiation of electromagnetic waves in the submillimeter range: nonlinear mixing of different frequencies; semiconductor lasers; molecular lasers with optical pumping; relativistic electron beams in a magnetic field as submillimeter radiation sources; submillimeter radiation sources on the basis of SHF classical electrovacuum devices - are considered. The designs of generator systems and their specifications are presented. The main parameters of electromagnetic radiation of different sources, such as: power, stability, frequency, tuning range - are presented. The methods of improving sources and electromagnetic radiation parameters are proposed. The examples of possible applications of submillimeter radiation in different spheres of science and technology are given [ru

  12. Molecular fountain.

    Energy Technology Data Exchange (ETDEWEB)

    Strecker, Kevin E.; Chandler, David W.

    2009-09-01

    A molecular fountain directs slowly moving molecules against gravity to further slow them to translational energies that they can be trapped and studied. If the molecules are initially slow enough they will return some time later to the position from which they were launched. Because this round trip time can be on the order of a second a single molecule can be observed for times sufficient to perform Hz level spectroscopy. The goal of this LDRD proposal was to construct a novel Molecular Fountain apparatus capable of producing dilute samples of molecules at near zero temperatures in well-defined user-selectable, quantum states. The slowly moving molecules used in this research are produced by the previously developed Kinematic Cooling technique, which uses a crossed atomic and molecular beam apparatus to generate single rotational level molecular samples moving slowly in the laboratory reference frame. The Kinematic Cooling technique produces cold molecules from a supersonic molecular beam via single collisions with a supersonic atomic beam. A single collision of an atom with a molecule occurring at the correct energy and relative velocity can cause a small fraction of the molecules to move very slowly vertically against gravity in the laboratory. These slowly moving molecules are captured by an electrostatic hexapole guiding field that both orients and focuses the molecules. The molecules are focused into the ionization region of a time-of-flight mass spectrometer and are ionized by laser radiation. The new molecular fountain apparatus was built utilizing a new design for molecular beam apparatus that has allowed us to miniaturize the apparatus. This new design minimizes the volumes and surface area of the machine allowing smaller pumps to maintain the necessary background pressures needed for these experiments.

  13. Source Water Protection Contaminant Sources

    Data.gov (United States)

    Iowa State University GIS Support and Research Facility — Simplified aggregation of potential contaminant sources used for Source Water Assessment and Protection. The data is derived from IDNR, IDALS, and US EPA program...

  14. Molecular docking.

    Science.gov (United States)

    Morris, Garrett M; Lim-Wilby, Marguerita

    2008-01-01

    Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand-protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings. Docking can be used to perform virtual screening on large libraries of compounds, rank the results, and propose structural hypotheses of how the ligands inhibit the target, which is invaluable in lead optimization. The setting up of the input structures for the docking is just as important as the docking itself, and analyzing the results of stochastic search methods can sometimes be unclear. This chapter discusses the background and theory of molecular docking software, and covers the usage of some of the most-cited docking software.

  15. Molecular modeling

    Directory of Open Access Journals (Sweden)

    Aarti Sharma

    2009-01-01

    Full Text Available The use of computational chemistry in the development of novel pharmaceuticals is becoming an increasingly important tool. In the past, drugs were simply screened for effectiveness. The recent advances in computing power and the exponential growth of the knowledge of protein structures have made it possible for organic compounds to be tailored to decrease the harmful side effects and increase the potency. This article provides a detailed description of the techniques employed in molecular modeling. Molecular modeling is a rapidly developing discipline, and has been supported by the dramatic improvements in computer hardware and software in recent years.

  16. Positron sources

    International Nuclear Information System (INIS)

    Chehab, R.

    1994-01-01

    A tentative survey of positron sources is given. Physical processes on which positron generation is based are indicated and analyzed. Explanation of the general features of electromagnetic interactions and nuclear β + decay makes it possible to predict the yield and emittance for a given optical matching system between the positron source and the accelerator. Some kinds of matching systems commonly used - mainly working with solenoidal field - are studied and the acceptance volume calculated. Such knowledge is helpful in comparing different matching systems. Since for large machines, a significant distance exists between the positron source and the experimental facility, positron emittance has to be preserved during beam transfer over large distances and methods used for that purpose are indicated. Comparison of existing positron sources leads to extrapolation to sources for future linear colliders. Some new ideas associated with these sources are also presented. (orig.)

  17. Molecular spectroscopy

    International Nuclear Information System (INIS)

    Kokh, Eh.; Zonntag, B.

    1981-01-01

    The latest investigation results on molecular spectroscopy with application of synchrotron radiation in the region of vacuum ultraviolet are generalized. Some results on investigation of excited, superexcited and ionized molecule states with the use of adsorption spectroscopy, photoelectron spectroscopy, by fluorescent and mass-spectrometric methods are considered [ru

  18. Molecular Foundry

    Science.gov (United States)

    . New Study Indicates Greater Capacity for Carbon Storage in the Earth's Subsurface A team of Foundry minerals which make up the dominant clays in the Earth's deep subsurface. Doubling Down on Energy Storage identify molecular components within small volumes of biological samples, such as blood or urine. Industry

  19. Molecular farming

    NARCIS (Netherlands)

    Merck, K.B.; Vereijken, J.M.

    2006-01-01

    Molecular Farming is a new and emerging technology that promises relatively cheap and flexible production of large quantities of pharmaceuticals in genetically modified plants. Many stakeholders are involved in the production of pharmaceuticals in plants, which complicates the discussion on the

  20. Molecular gastronomy

    Science.gov (United States)

    This, Hervé

    2005-01-01

    For centuries, cooks have been applying recipes without looking for the mechanisms of the culinary transformations. A scientific discipline that explores these changes from raw ingredients to eating the final dish, is developing into its own field, termed molecular gastronomy. Here, one of the founders of the discipline discusses its aims and importance.

  1. Molecular Star

    Indian Academy of Sciences (India)

    In molecular self-assembly, molecules put themselves together in a predefined way ... work has been already published in Chemistry- A European Jour- nal in the September ... prevalent in matter ranging from atoms to molecules to biomolecules; it is also ... erate chemical forces are reversible and dynamic in nature mean-.

  2. Molecular ferromagnetism

    International Nuclear Information System (INIS)

    Epstein, A.J.

    1990-01-01

    This past year has been one of substantial advancement in both the physics and chemistry of molecular and polymeric ferromagnets. The specific heat studies of (DMeFc)(TCNE) have revealed a cusp at the three-dimensional ferromagnetic transition temperature with a crossover to primarily 1-D behavior at higher temperatures. This paper discusses these studies

  3. Sources management

    International Nuclear Information System (INIS)

    Mansoux, H.; Gourmelon; Scanff, P.; Fournet, F.; Murith, Ch.; Saint-Paul, N.; Colson, P.; Jouve, A.; Feron, F.; Haranger, D.; Mathieu, P.; Paycha, F.; Israel, S.; Auboiroux, B.; Chartier, P.

    2005-01-01

    Organized by the section of technical protection of the French society of radiation protection ( S.F.R.P.), these two days had for objective to review the evolution of the rule relative to the sources of ionising radiations 'sealed and unsealed radioactive sources, electric generators'. They addressed all the actors concerned by the implementation of the new regulatory system in the different sectors of activities ( research, medicine and industry): Authorities, manufacturers, and suppliers of sources, holders and users, bodies involved in the approval of sources, carriers. (N.C.)

  4. Sourcing Excellence

    DEFF Research Database (Denmark)

    Adeyemi, Oluseyi

    2011-01-01

    Sourcing Excellence is one of the key performance indicators (KPIs) in this world of ever changing sourcing strategies. Manufacturing companies need to access and diagnose the reliability and competencies of existing suppliers in order to coordinate and develop them. This would help in managing...

  5. Molecular beam kinetics

    International Nuclear Information System (INIS)

    Behrens, R. Jr.

    1975-11-01

    The design of a crossed molecular beam ''supermachine'' for neutral--neutral collisions is discussed. The universal electron bombardment ionizer, mass filter, and ion detection system of the detector, the supersonic nozzle sources, the differential pumping arrangement for the sources and detector, the time-of-flight detection of scattered products, and the overall configuration of the apparatus are described. The elastic scattering of two systems, CH 4 + Ar and NH 3 + Ar, has been measured using the supermachine with two supersonic nozzle sources. The rainbow structure and the interference oscillations are seen in each system. The best fit to the data was found using a Morse--Spline--Van der Waals (MSV) potential. The three potential parameters epsilon, r/sub m/, and β were found to be 2.20(+-0.04) x 10 -14 ergs, 3.82(+-0.04)A, and 7.05 +- 0.20 for CH 4 + Ar, and 2.21(+-0.04) x 10 -14 ergs 3.93 (+-0.05)A, and 8.45 +- 0.30 for NH 3 + Ar. A new phenomenon in crossed molecular beams of condensation of a molecule on a cluster to form a complex was observed. A bromine molecule condensed on clusters of chlorine (Cl 2 )/sub chi/ and ammonia (NH 3 )/sub chi/. The value of chi for measurements in these experiments ranges from 7 to 40 for chlorine clusters and from 10 to 70 ammonia clusters

  6. Positron sources

    International Nuclear Information System (INIS)

    Chehab, R.

    1989-01-01

    A tentative survey of positron sources is given. Physical processes on which positron generation is based are indicated and analyzed. Explanation of the general features of electromagnetic interactions and nuclear β + decay makes it possible to predict the yield and emittance for a given optical matching system between the positron source and the accelerator. Some kinds of matching systems commonly used - mainly working with solenoidal fields - are studied and the acceptance volume calculated. Such knowledge is helpful in comparing different matching systems. Since for large machines, a significant distance exists between the positron source and the experimental facility, positron emittance has to be preserved during beam transfer over large distances and methods used for that purpose are indicated. Comparison of existing positron sources leads to extrapolation to sources for future linear colliders

  7. Molecular Modelling

    Directory of Open Access Journals (Sweden)

    Aarti Sharma

    2009-12-01

    Full Text Available

    The use of computational chemistry in the development of novel pharmaceuticals is becoming an increasingly important
    tool. In the past, drugs were simply screened for effectiveness. The recent advances in computing power and
    the exponential growth of the knowledge of protein structures have made it possible for organic compounds to tailored to
    decrease harmful side effects and increase the potency. This article provides a detailed description of the techniques
    employed in molecular modeling. Molecular modelling is a rapidly developing discipline, and has been supported from
    the dramatic improvements in computer hardware and software in recent years.

  8. Molecular scale

    Directory of Open Access Journals (Sweden)

    Christopher H. Childers

    2016-03-01

    Full Text Available This manuscript demonstrates the molecular scale cure rate dependence of di-functional epoxide based thermoset polymers cured with amines. A series of cure heating ramp rates were used to determine the influence of ramp rate on the glass transition temperature (Tg and sub-Tg transitions and the average free volume hole size in these systems. The networks were comprised of 3,3′-diaminodiphenyl sulfone (33DDS and diglycidyl ether of bisphenol F (DGEBF and were cured at ramp rates ranging from 0.5 to 20 °C/min. Differential scanning calorimetry (DSC and NIR spectroscopy were used to explore the cure ramp rate dependence of the polymer network growth, whereas broadband dielectric spectroscopy (BDS and free volume hole size measurements were used to interrogate networks’ molecular level structural variations upon curing at variable heating ramp rates. It was found that although the Tg of the polymer matrices was similar, the NIR and DSC measurements revealed a strong correlation for how these networks grow in relation to the cure heating ramp rate. The free volume analysis and BDS results for the cured samples suggest differences in the molecular architecture of the matrix polymers due to cure heating rate dependence.

  9. Molecular phylogeny of some avian species using Cytochrome b gene sequence analysis

    Science.gov (United States)

    Awad, A; Khalil, S. R; Abd-Elhakim, Y. M

    2015-01-01

    Veritable identification and differentiation of avian species is a vital step in conservative, taxonomic, forensic, legal and other ornithological interventions. Therefore, this study involved the application of molecular approach to identify some avian species i.e. Chicken (Gallus gallus), Muskovy duck (Cairina moschata), Japanese quail (Coturnix japonica), Laughing dove (Streptopelia senegalensis), and Rock pigeon (Columba livia). Genomic DNA was extracted from blood samples and partial sequence of the mitochondrial cytochrome b gene (358 bp) was amplified and sequenced using universal primers. Sequences alignment and phylogenetic analyses were performed by CLC main workbench program. The obtained five sequences were deposited in GenBank and compared with those previously registered in GenBank. The similarity percentage was 88.60% between Gallus gallus and Coturnix japonica and 80.46% between Gallus gallus and Columba livia. The percentage of identity between the studied species and GenBank species ranged from 77.20% (Columba oenas and Anas platyrhynchos) to 100% (Gallus gallus and Gallus sonneratii, Coturnix coturnix and Coturnix japonica, Meleagris gallopavo and Columba livia). Amplification of the partial sequence of mitochondrial cytochrome b gene proved to be practical for identification of an avian species unambiguously. PMID:27175180

  10. QuBiLS-MAS, open source multi-platform software for atom- and bond-based topological (2D) and chiral (2.5D) algebraic molecular descriptors computations.

    Science.gov (United States)

    Valdés-Martiní, José R; Marrero-Ponce, Yovani; García-Jacas, César R; Martinez-Mayorga, Karina; Barigye, Stephen J; Vaz d'Almeida, Yasser Silveira; Pham-The, Hai; Pérez-Giménez, Facundo; Morell, Carlos A

    2017-06-07

    In previous reports, Marrero-Ponce et al. proposed algebraic formalisms for characterizing topological (2D) and chiral (2.5D) molecular features through atom- and bond-based ToMoCoMD-CARDD (acronym for Topological Molecular Computational Design-Computer Aided Rational Drug Design) molecular descriptors. These MDs codify molecular information based on the bilinear, quadratic and linear algebraic forms and the graph-theoretical electronic-density and edge-adjacency matrices in order to consider atom- and bond-based relations, respectively. These MDs have been successfully applied in the screening of chemical compounds of different therapeutic applications ranging from antimalarials, antibacterials, tyrosinase inhibitors and so on. To compute these MDs, a computational program with the same name was initially developed. However, this in house software barely offered the functionalities required in contemporary molecular modeling tasks, in addition to the inherent limitations that made its usability impractical. Therefore, the present manuscript introduces the QuBiLS-MAS (acronym for Quadratic, Bilinear and N-Linear mapS based on graph-theoretic electronic-density Matrices and Atomic weightingS) software designed to compute topological (0-2.5D) molecular descriptors based on bilinear, quadratic and linear algebraic forms for atom- and bond-based relations. The QuBiLS-MAS module was designed as standalone software, in which extensions and generalizations of the former ToMoCoMD-CARDD 2D-algebraic indices are implemented, considering the following aspects: (a) two new matrix normalization approaches based on double-stochastic and mutual probability formalisms; (b) topological constraints (cut-offs) to take into account particular inter-atomic relations; (c) six additional atomic properties to be used as weighting schemes in the calculation of the molecular vectors; (d) four new local-fragments to consider molecular regions of interest; (e) number of lone-pair electrons in

  11. Spintronics: The molecular way

    Science.gov (United States)

    Cornia, Andrea; Seneor, Pierre

    2017-05-01

    Molecular spintronics is an interdisciplinary field at the interface between organic spintronics, molecular magnetism, molecular electronics and quantum computing, which is advancing fast and promises large technological payoffs.

  12. Future Synchrotron Radiation Sources

    CERN Document Server

    Winick, Herman

    2003-01-01

    Sources of synchrotron radiation (also called synchrotron light) and their associated research facilities have experienced a spectacular growth in number, performance, and breadth of application in the past two to three decades. In 1978 there were eleven electron storage rings used as light sources. Three of these were small rings, all below 500 mega-electron volts (MeV), dedicated to this purpose; the others, with energy up to 5 giga-electron volts (GeV), were used parasitically during the operation of the ring for high energy physics research. In addition, at that time synchrotron radiation from nine cyclic electron synchrotrons, with energy up to 5 GeV, was also used parasitically. At present no cyclic synchrotrons are used, while about 50 electron storage rings are in operation around the world as fully dedicated light sources for basic and applied research in a wide variety of fields. Among these fields are structural molecular biology, molecular environmental science, materials, analytic chemistry, micr...

  13. Molecular nanomagnets

    CERN Document Server

    Gatteschi, Dante; Villain, Jacques

    2006-01-01

    Nanomagnetism is a rapidly expanding area of research which appears to be able to provide novel applications. Magnetic molecules are at the very bottom of the possible size of nanomagnets and they provide a unique opportunity to observe the coexistence of classical and quantum properties. The discovery in the early 90's that a cluster comprising twelve manganese ions shows hysteresis of molecular origin, and later proved evidence of quantum effects, opened a new research area whichis still flourishing through the collaboration of chemists and physicists. This book is the first attempt to cover

  14. Molecular plasmonics

    CERN Document Server

    Fritzsche, Wolfgang

    2014-01-01

    Adopting a novel approach, this book provides a unique ""molecular perspective"" on plasmonics, concisely presenting the fundamentals and applications in a way suitable for beginners entering this hot field as well as for experienced researchers and practitioners. It begins by introducing readers to the optical effects that occur at the nanoscale and particularly their modification in the presence of biomolecules, followed by a concise yet thorough overview of the different methods for the actual fabrication of nanooptical materials. Further chapters address the relevant nanooptics, as well as

  15. Application of Molecular Typing Results in Source Attribution Models: The Case of Multiple Locus Variable Number Tandem Repeat Analysis (MLVA) of Salmonella Isolates Obtained from Integrated Surveillance in Denmark

    DEFF Research Database (Denmark)

    de Knegt, Leonardo; Pires, Sara Monteiro; Löfström, Charlotta

    2016-01-01

    , and antibiotic resistance profiles for the Salmonella source attribution, and assess the utility of the results for the food safety decisionmakers. Full and simplified MLVA schemes from surveillance data were tested, and model fit and consistency of results were assessed using statistical measures. We conclude...

  16. Neutron source

    International Nuclear Information System (INIS)

    Cason, J.L. Jr.; Shaw, C.B.

    1975-01-01

    A neutron source which is particularly useful for neutron radiography consists of a vessel containing a moderating media of relatively low moderating ratio, a flux trap including a moderating media of relatively high moderating ratio at the center of the vessel, a shell of depleted uranium dioxide surrounding the moderating media of relatively high moderating ratio, a plurality of guide tubes each containing a movable source of neutrons surrounding the flux trap, a neutron shield surrounding one part of each guide tube, and at least one collimator extending from the flux trap to the exterior of the neutron source. The shell of depleted uranium dioxide has a window provided with depleted uranium dioxide shutters for each collimator. Reflectors are provided above and below the flux trap and on the guide tubes away from the flux trap

  17. Crowd Sourcing.

    Science.gov (United States)

    Baum, Neil

    2016-01-01

    The Internet has contributed new words and slang to our daily vernacular. A few terms, such as tweeting, texting, sexting, blogging, and googling, have become common in most vocabularies and in many languages, and are now included in the dictionary. A new buzzword making the rounds in industry is crowd sourcing, which involves outsourcing an activity, task, or problem by sending it to people or groups outside a business or a practice. Crowd sourcing allows doctors and practices to tap the wisdom of many instead of relying only on the few members of their close-knit group. This article defines "crowd sourcing," offers examples, and explains how to get started with this approach that can increase your ability to finish a task or solve problems that you don't have the time or expertise to accomplish.

  18. Synchrotron radiation sources

    Energy Technology Data Exchange (ETDEWEB)

    van Steenbergen, A.

    1979-01-01

    As a result of the exponential growth of the utilization of synchrotron radiation for research in the domain of the material sciences, atomic and molecular physics, biology and technology, a major construction activity has been generated towards new dedicated electron storage rings, designed optimally for synchrotron radiation applications, also, expansion programs are underway at the existing facilities, such as DORIS, SPEAR, and VEPP. In this report the basic properties of synchrotron radiation will be discussed, a short overview will be given of the existing and new facilities, some aspects of the optimization of a structure for a synchrotron radiation source will be discussed and the addition of wigglers and undulators for spectrum enhancement will be described. Finally, some parameters of an optimized synchrotron radiation source will be given.

  19. Energy sources

    International Nuclear Information System (INIS)

    Vajda, Gy.

    1998-01-01

    A comprehensive review is presented of the available sources of energy in the world is presented. About 80 percent of primary energy utilization is based on fossile fuels, and their dominant role is not expected to change in the foreseeable future. Data are given on petroleum, natural gas and coal based power production. The role and economic aspects of nuclear power are analyzed. A brief summary of renewable energy sources is presented. The future prospects of the world's energy resources are discussed, and the special position of Hungary regarding fossil, nuclear and renewable energy and the country's energy potential is evaluated. (R.P.)

  20. Ion source

    International Nuclear Information System (INIS)

    1977-01-01

    The specifications of a set of point-shape electrodes of non-corrodable material that can hold a film of liquid material of equal thickness is described. Contained in a jacket, this set forms an ion source. The electrode is made of tungsten with a glassy carbon layer for insulation and an outer layer of aluminium-oxide ceramic material

  1. Progress on molecular imaging

    International Nuclear Information System (INIS)

    Chen Quan; Zhang Yongxue

    2011-01-01

    Molecular imaging is a new era of medical imaging,which can non-invasively monitor biological processes at the cellular and molecular level in vivo, including molecular imaging of nuclear medicine, magnetic resonance molecular imaging, ultrasound molecular imaging,optical molecular imaging and molecular imaging with X-ray. Recently, with the development of multi-subjects amalgamation, multimodal molecular imaging technology has been applied in clinical imaging, such as PET-CT and PET-MRI. We believe that with development of molecular probe and multi-modal imaging, more and more molecular imaging techniques will be applied in clinical diagnosis and treatment. (authors)

  2. Orphan sources

    International Nuclear Information System (INIS)

    Pust, R.; Urbancik, L.

    2008-01-01

    The presentation describes how the stable detection systems (hereinafter referred to as S DS ) have contributed to reveal the uncontrolled sources of ionizing radiation on the territory of the State Office for Nuclear Safety (SONS) Brno Regional Centre (RC Brno). It also describes the emergencies which were solved by or in which the workers from the Brno. Regional Centre participated in. The contribution is divided into the following chapters: A. SDS systems installed on the territory of SONS RC Brno; B. Selected unusual emergencies; C. Comments to individual emergencies; D. Aspects of SDS operation in term of their users; E. Aspects of SDS operation and related activities in term of radiation protection; F. Current state of orphan sources. (authors)

  3. Tritium sources

    International Nuclear Information System (INIS)

    Glodic, S.; Boreli, F.

    1993-01-01

    Tritium is the only radioactive isotope of hydrogen. It directly follows the metabolism of water and it can be bound into genetic material, so it is very important to control levels of contamination. In order to define the state of contamination it is necessary to establish 'zero level', i.e. actual global inventory. The importance of tritium contamination monitoring increases with the development of fusion power installations. Different sources of tritium are analyzed and summarized in this paper. (author)

  4. Source rock

    Directory of Open Access Journals (Sweden)

    Abubakr F. Makky

    2014-03-01

    Full Text Available West Beni Suef Concession is located at the western part of Beni Suef Basin which is a relatively under-explored basin and lies about 150 km south of Cairo. The major goal of this study is to evaluate the source rock by using different techniques as Rock-Eval pyrolysis, Vitrinite reflectance (%Ro, and well log data of some Cretaceous sequences including Abu Roash (E, F and G members, Kharita and Betty formations. The BasinMod 1D program is used in this study to construct the burial history and calculate the levels of thermal maturity of the Fayoum-1X well based on calibration of measured %Ro and Tmax against calculated %Ro model. The calculated Total Organic Carbon (TOC content from well log data compared with the measured TOC from the Rock-Eval pyrolysis in Fayoum-1X well is shown to match against the shale source rock but gives high values against the limestone source rock. For that, a new model is derived from well log data to calculate accurately the TOC content against the limestone source rock in the study area. The organic matter existing in Abu Roash (F member is fair to excellent and capable of generating a significant amount of hydrocarbons (oil prone produced from (mixed type I/II kerogen. The generation potential of kerogen in Abu Roash (E and G members and Betty formations is ranging from poor to fair, and generating hydrocarbons of oil and gas prone (mixed type II/III kerogen. Eventually, kerogen (type III of Kharita Formation has poor to very good generation potential and mainly produces gas. Thermal maturation of the measured %Ro, calculated %Ro model, Tmax and Production index (PI indicates that Abu Roash (F member exciting in the onset of oil generation, whereas Abu Roash (E and G members, Kharita and Betty formations entered the peak of oil generation.

  5. Radioactive source

    International Nuclear Information System (INIS)

    Drabkina, L.E.; Mazurek, V.; Myascedov, D.N.; Prokhorov, P.; Kachalov, V.A.; Ziv, D.M.

    1976-01-01

    A radioactive layer in a radioactive source is sealed by the application of a sealing layer on the radioactive layer. The sealing layer can consist of a film of oxide of titanium, tin, zirconium, aluminum, or chromium. Preferably, the sealing layer is pure titanium dioxide. The radioactive layer is embedded in a finish enamel which, in turn, is on a priming enamel which surrounds a substrate

  6. Muon sources

    International Nuclear Information System (INIS)

    Parsa, Z.

    2001-01-01

    A full high energy muon collider may take considerable time to realize. However, intermediate steps in its direction are possible and could help facilitate the process. Employing an intense muon source to carry out forefront low energy research, such as the search for muon-number non-conservation, represents one interesting possibility. For example, the MECO proposal at BNL aims for 2 x 10 -17 sensitivity in their search for coherent muon-electron conversion in the field of a nucleus. To reach that goal requires the production, capture and stopping of muons at an unprecedented 10 11 μ/sec. If successful, such an effort would significantly advance the state of muon technology. More ambitious ideas for utilizing high intensity muon sources are also being explored. Building a muon storage ring for the purpose of providing intense high energy neutrino beams is particularly exciting.We present an overview of muon sources and example of a muon storage ring based Neutrino Factory at BNL with various detector location possibilities

  7. Guidelines on the use of molecular genetics in reintroduction programs

    Science.gov (United States)

    Michael K. Schwartz

    2005-01-01

    The use of molecular genetics can play a key role in reintroduction efforts. Prior to the introduction of any individuals, molecular genetics can be used to identify the most appropriate source population for the reintroduction, ensure that no relic populations exist in the reintroduction area, and guide captive breeding programs. The use of molecular genetics post-...

  8. Molecular Electronic Terms and Molecular Orbital Configurations.

    Science.gov (United States)

    Mazo, R. M.

    1990-01-01

    Discussed are the molecular electronic terms which can arise from a given electronic configuration. Considered are simple cases, molecular states, direct products, closed shells, and open shells. Two examples are provided. (CW)

  9. An ab initio molecular

    Indian Academy of Sciences (India)

    mechanisms of two molecular crystals: An ab initio molecular dynamics ... for Computation in Molecular and Materials Science and Department of Chemistry, School of ..... NSAF Foundation of National Natural Science Foun- ... Matter 14 2717.

  10. A recycling molecular beam reactor

    International Nuclear Information System (INIS)

    Prada-Silva, G.; Haller, G.L.; Fenn, J.B.

    1974-01-01

    In a Recycling Molecular Beam Reactor, RMBR, a beam of reactant gas molecules is formed from a supersonic free jet. After collision with a target the molecules pass through the vacuum pumps and are returned to the nozzle source. Continuous recycling permits the integration of very small reaction probabilities into measurable conversions which can be analyzed by gas chromatography. Some preliminary experiments have been carried out on the isomerization of cyclopropane

  11. Optical Pumping of Molecular Gases

    Science.gov (United States)

    1976-04-01

    ser emission ott a The typical experimental apparatus is shown i.- Fig. *series of green and yellow molecular B-X’-basnd transi- 2. For B-bantd optical...with A, at 0. 473 pim and that Na2 may operate as a flash -lamp -pumped laser X,... at 0. 54 umn the Doppler widths are AwD - 12.42 source with buffer

  12. Gas flow parameter determination by molecular beam method

    International Nuclear Information System (INIS)

    Zarvin, A.E.; Sharafutdinov, R.G.

    1977-01-01

    This paper describes a molecular-beam system intended for studying nonequilibrium processes in supersonic rarefied gas flows. The system represented is a small molecular beam source placed inside the low intensity wind tunnel of the Institute of Thermophysics, Siberian Branch of the USSR Academy of Sciences. The time-of-flight method is used for measuring molecular velocity distribution functions on molecular beam axis. (Auth.)

  13. Evaluation of the health impact of aerosols emitted from different combustion sources: Comprehensive characterization of the aerosol physicochemical properties as well as the molecular biological and toxicological effects of the aerosols on human lung cells and macrophages.

    Science.gov (United States)

    Zimmermann, R.; Dittmar, G.; Kanashova, T.; Buters, J.; Öder, S.; Paur, H. R.; Mülhopt, S.; Dilger, M.; Weiss, C.; Harndorf, H.; Stengel, B.; Hirvonen, M. R.; Jokiniemi, J.; Hiller, K.; Sapcariu, S.; Sippula, O.; Streibel, T.; Karg, E.; Weggler, B.; Schnelle-Kreis, J.; Lintelmann, J.; Sklorz, M.; Orasche, J.; Müller, L.; Passig, J.; Gröger, T.; Jalava, P. I.; Happo, M.; Uski, O.

    2017-12-01

    . Detailed analyses suggest a large difference in relative toxicity for different combustion sources. Recently the cell experiments were successively evaluated and verified by animal exposure tests. This is important to develop a reliable animal-test free-monitoring method for aerosol-induced health effects.

  14. Isotopic and molecular fractionation in combustion; three routes to molecular marker validation, including direct molecular 'dating' (GC/AMS)

    Science.gov (United States)

    Currie, L. A.; Klouda, G. A.; Benner, B. A.; Garrity, K.; Eglinton, T. I.

    The identification of unique isotopic, elemental, and molecular markers for sources of combustion aerosol has growing practical importance because of the potential effects of fine particle aerosol on health, visibility and global climate. It is urgent, therefore, that substantial efforts be directed toward the validation of assumptions involving the use of such tracers for source apportionment. We describe here three independent routes toward carbonaceous aerosol molecular marker identification and validation: (1) tracer regression and multivariate statistical techniques applied to field measurements of mixed source, carbonaceous aerosols; (2) a new development in aerosol 14C metrology: direct, pure compound accelerator mass spectrometry (AMS) by off-line GC/AMS ('molecular dating'); and (3) direct observation of isotopic and molecular source emissions during controlled laboratory combustion of specific fuels. Findings from the combined studies include: independent support for benzo( ghi)perylene as a motor vehicle tracer from the first (statistical) and second (direct 'dating') studies; a new indication, from the third (controlled combustion) study, of a relation between 13C isotopic fractionation and PAH molecular fractionation, also linked with fuel and stage of combustion; and quantitative data showing the influence of both fuel type and combustion conditions on the yields of such species as elemental carbon and PAH, reinforcing the importance of exercising caution when applying presumed conservative elemental or organic tracers to fossil or biomass burning field data as in the first study.

  15. Molecular HIV screening.

    Science.gov (United States)

    Bourlet, Thomas; Memmi, Meriam; Saoudin, Henia; Pozzetto, Bruno

    2013-09-01

    Nuclear acid testing is more and more used for the diagnosis of infectious diseases. This paper focuses on the use of molecular tools for HIV screening. The term 'screening' will be used under the meaning of first-line HIV molecular techniques performed on a routine basis, which excludes HIV molecular tests designed to confirm or infirm a newly discovered HIV-seropositive patient or other molecular tests performed for the follow-up of HIV-infected patients. The following items are developed successively: i) presentation of the variety of molecular tools used for molecular HIV screening, ii) use of HIV molecular tools for the screening of blood products, iii) use of HIV molecular tools for the screening of organs and tissue from human origin, iv) use of HIV molecular tools in medically assisted procreation and v) use of HIV molecular tools in neonates from HIV-infected mothers.

  16. Understanding molecular structure from molecular mechanics.

    Science.gov (United States)

    Allinger, Norman L

    2011-04-01

    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  17. Cancer Stratification by Molecular Imaging

    Directory of Open Access Journals (Sweden)

    Justus Weber

    2015-03-01

    Full Text Available The lack of specificity of traditional cytotoxic drugs has triggered the development of anticancer agents that selectively address specific molecular targets. An intrinsic property of these specialized drugs is their limited applicability for specific patient subgroups. Consequently, the generation of information about tumor characteristics is the key to exploit the potential of these drugs. Currently, cancer stratification relies on three approaches: Gene expression analysis and cancer proteomics, immunohistochemistry and molecular imaging. In order to enable the precise localization of functionally expressed targets, molecular imaging combines highly selective biomarkers and intense signal sources. Thus, cancer stratification and localization are performed simultaneously. Many cancer types are characterized by altered receptor expression, such as somatostatin receptors, folate receptors or Her2 (human epidermal growth factor receptor 2. Similar correlations are also known for a multitude of transporters, such as glucose transporters, amino acid transporters or hNIS (human sodium iodide symporter, as well as cell specific proteins, such as the prostate specific membrane antigen, integrins, and CD20. This review provides a comprehensive description of the methods, targets and agents used in molecular imaging, to outline their application for cancer stratification. Emphasis is placed on radiotracers which are used to identify altered expression patterns of cancer associated markers.

  18. Molecular sensors and molecular logic gates

    International Nuclear Information System (INIS)

    Georgiev, N.; Bojinov, V.

    2013-01-01

    Full text: The rapid grow of nanotechnology field extended the concept of a macroscopic device to the molecular level. Because of this reason the design and synthesis of (supra)-molecular species capable of mimicking the functions of macroscopic devices are currently of great interest. Molecular devices operate via electronic and/or nuclear rearrangements and, like macroscopic devices, need energy to operate and communicate between their elements. The energy needed to make a device work can be supplied as chemical energy, electrical energy, or light. Luminescence is one of the most useful techniques to monitor the operation of molecular-level devices. This fact determinates the synthesis of novel fluorescence compounds as a considerable and inseparable part of nanoscience development. Further miniaturization of semiconductors in electronic field reaches their limit. Therefore the design and construction of molecular systems capable of performing complex logic functions is of great scientific interest now. In semiconductor devices the logic gates work using binary logic, where the signals are encoded as 0 and 1 (low and high current). This process is executable on molecular level by several ways, but the most common are based on the optical properties of the molecule switches encoding the low and high concentrations of the input guest molecules and the output fluorescent intensities with binary 0 and 1 respectively. The first proposal to execute logic operations at the molecular level was made in 1988, but the field developed only five years later when the analogy between molecular switches and logic gates was experimentally demonstrated by de Silva. There are seven basic logic gates: AND, OR, XOR, NOT, NAND, NOR and XNOR and all of them were achieved by molecules, the fluorescence switching as well. key words: fluorescence, molecular sensors, molecular logic gates

  19. Molecular Diagnostic Tests for Microsporidia

    Directory of Open Access Journals (Sweden)

    Kaya Ghosh

    2009-01-01

    Full Text Available The Microsporidia are a ubiquitous group of eukaryotic obligate intracellular parasites which were recognized over 100 years ago with the description of Nosema bombycis, a parasite of silkworms. It is now appreciated that these organisms are related to the Fungi. Microsporidia infect all major animal groups most often as gastrointestinal pathogens; however they have been reported from every tissue and organ, and their spores are common in environmental sources such as ditch water. Several different genera of these organisms infect humans, but the majority of infections are due to either Enterocytozoon bieneusi or Encephalitozoon species. These pathogens can be difficult to diagnose, but significant progress has been made in the last decade in the development of molecular diagnostic reagents for these organisms. This report reviews the molecular diagnostic tests that have been described for the identification of the microsporidia that infect humans.

  20. Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

    Directory of Open Access Journals (Sweden)

    Enis Afgan

    Full Text Available Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise.We designed and implemented the Genomics Virtual Laboratory (GVL as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic.This paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints, and explore the value added to the research community through the suite of services and resources provided by our implementation.

  1. Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.

    Science.gov (United States)

    Afgan, Enis; Sloggett, Clare; Goonasekera, Nuwan; Makunin, Igor; Benson, Derek; Crowe, Mark; Gladman, Simon; Kowsar, Yousef; Pheasant, Michael; Horst, Ron; Lonie, Andrew

    2015-01-01

    Analyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s) enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise. We designed and implemented the Genomics Virtual Laboratory (GVL) as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook) or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au) and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic. This paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints, and explore the value added to the research community through the suite of services and resources provided by our implementation.

  2. Low-Cost Virtual Laboratory Workbench for Electronic Engineering

    Science.gov (United States)

    Achumba, Ifeyinwa E.; Azzi, Djamel; Stocker, James

    2010-01-01

    The laboratory component of undergraduate engineering education poses challenges in resource constrained engineering faculties. The cost, time, space and physical presence requirements of the traditional (real) laboratory approach are the contributory factors. These resource constraints may mitigate the acquisition of meaningful laboratory…

  3. RemBench: A Digital Workbench for Rembrandt Research

    NARCIS (Netherlands)

    Verberne, Suzan; Van Leeuwen, Rudie; Gerritsen, G.H.; Boves, Lou

    2016-01-01

    In this paper, we present RemBench, a search engine for research into the life and works of Rembrandt van Rijn. RemBench combines the data from four different databases behind one interface using federated search technology. Metadata filtering is enabled through faceted search. RemBench enables art

  4. SIGNATURE: A workbench for gene expression signature analysis

    Directory of Open Access Journals (Sweden)

    Chang Jeffrey T

    2011-11-01

    Full Text Available Abstract Background The biological phenotype of a cell, such as a characteristic visual image or behavior, reflects activities derived from the expression of collections of genes. As such, an ability to measure the expression of these genes provides an opportunity to develop more precise and varied sets of phenotypes. However, to use this approach requires computational methods that are difficult to implement and apply, and thus there is a critical need for intelligent software tools that can reduce the technical burden of the analysis. Tools for gene expression analyses are unusually difficult to implement in a user-friendly way because their application requires a combination of biological data curation, statistical computational methods, and database expertise. Results We have developed SIGNATURE, a web-based resource that simplifies gene expression signature analysis by providing software, data, and protocols to perform the analysis successfully. This resource uses Bayesian methods for processing gene expression data coupled with a curated database of gene expression signatures, all carried out within a GenePattern web interface for easy use and access. Conclusions SIGNATURE is available for public use at http://genepattern.genome.duke.edu/signature/.

  5. Development of an ATR Workbench for SAR Imagery

    Science.gov (United States)

    2002-12-01

    underlying the automation of target recognition, such as pattern recognition, machine vision, artificial intelligence , etc., are still considered to be in...jacentes A l’automatisation de la reconnaissance des cibles, comme la reconnaissance des formes, la vision machine, l’intelligence artificielle , etc., en...left blank. xii DRDC Ottawa TR 2002-155 1 Introduction Creating intelligent systems capable of mimicking traits found in humans is a challenge that

  6. Identification of the source of histoplasmosis infection in two captive maras (Dolichotis patagonum from the same colony by using molecular and immunologic assays Identificación de la fuente de infección de histoplasmosis de dos maras (Dolichotis patagonum cautivas procedentes de la misma colonia, utilizando ensayos moleculares e inmunológicos

    Directory of Open Access Journals (Sweden)

    M. R. Reyes-Montes

    2009-06-01

    Full Text Available Histoplasma capsulatum was isolated from the spleen of a first infected mara (Dolichotis patagonum and from a second mara's liver and adrenal gland, both in the same colony at the Africam Safari, Puebla, Mexico. Studies of H. capsulatum isolates, using nested-PCR of a 100-kDa protein coding gene (Hcp100 fragment and a two-primer RAPDPCR method, suggest that these isolates were spreading in the environment of the maras' enclosure. By using a Dot- ELISA method, sera from mice inoculated with three homogenates of soil samples from the maras' enclosed space developed positive brown spot reactions to a purified H. capsulatum antigen, which identified the probable source of the maras' infection.Histoplasma capsulatum fue aislado del bazo de una primera mara (Dolichotis patagonum infectada y del hígado y la glándula suprarrenal de un segundo ejemplar, ambos de la misma colonia en el Africam Safari, Puebla, México. Los estudios de los aislamientos de H. capsulatum mediante PCR anidada para un fragmento del gen Hcp100 que codifica una proteína de 100 kDa y RAPD-PCR empleando doble iniciador sugieren que estos aislamientos estaban dispersos en el ambiente del refugio de las maras. Los sueros de ratones inoculados con tres homogenatos de muestras de suelo del refugio desarrollaron reacciones positivas a un antígeno purificado de H. capsulatum (manchas color castaño oscuro por el método de Dot-ELISA; con lo cual se identificó la probable fuente de infección de las maras.

  7. Basic molecular spectroscopy

    CERN Document Server

    Gorry, PA

    1985-01-01

    BASIC Molecular Spectroscopy discusses the utilization of the Beginner's All-purpose Symbolic Instruction Code (BASIC) programming language in molecular spectroscopy. The book is comprised of five chapters that provide an introduction to molecular spectroscopy through programs written in BASIC. The coverage of the text includes rotational spectra, vibrational spectra, and Raman and electronic spectra. The book will be of great use to students who are currently taking a course in molecular spectroscopy.

  8. Digitotalar dysmorphism: Molecular elucidation

    African Journals Online (AJOL)

    obtained for molecular studies. Since the distal arthrogryposes (DAs) are genetically heterogeneous, an unbiased approach to mutation ... Diseases and Molecular Medicine, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa, with an interest in molecular genetics of connective ...

  9. Artificial molecular motors

    NARCIS (Netherlands)

    Kassem, Salma; van Leeuwen, Thomas; Lubbe, Anouk S.; Wilson, Miriam R.; Feringa, Ben L.; Leigh, David A.

    2017-01-01

    Motor proteins are nature's solution for directing movement at the molecular level. The field of artificial molecular motors takes inspiration from these tiny but powerful machines. Although directional motion on the nanoscale performed by synthetic molecular machines is a relatively new

  10. Molecular identification and food source inference of constructive ...

    African Journals Online (AJOL)

    Ophiocordyceps sinensis is a precious and effectual Traditional Chinese Medicine, native to Tibetan Plateau. Its development originated from parasitization of Hirsutella sinensis to Hepialus larvae, which was deemed to be of great importance including feeding food habit. Hereby in the present, study on food resource ...

  11. The Chandra Source Catalog : Automated Source Correlation

    Science.gov (United States)

    Hain, Roger; Evans, I. N.; Evans, J. D.; Glotfelty, K. J.; Anderson, C. S.; Bonaventura, N. R.; Chen, J. C.; Davis, J. E.; Doe, S. M.; Fabbiano, G.; Galle, E.; Gibbs, D. G.; Grier, J. D.; Hall, D. M.; Harbo, P. N.; He, X.; Houck, J. C.; Karovska, M.; Lauer, J.; McCollough, M. L.; McDowell, J. C.; Miller, J. B.; Mitschang, A. W.; Morgan, D. L.; Nichols, J. S.; Nowak, M. A.; Plummer, D. A.; Primini, F. A.; Refsdal, B. L.; Rots, A. H.; Siemiginowska, A. L.; Sundheim, B. A.; Tibbetts, M. S.; Van Stone, D. W.; Winkelman, S. L.; Zografou, P.

    2009-01-01

    Chandra Source Catalog (CSC) master source pipeline processing seeks to automatically detect sources and compute their properties. Since Chandra is a pointed mission and not a sky survey, different sky regions are observed for a different number of times at varying orientations, resolutions, and other heterogeneous conditions. While this provides an opportunity to collect data from a potentially large number of observing passes, it also creates challenges in determining the best way to combine different detection results for the most accurate characterization of the detected sources. The CSC master source pipeline correlates data from multiple observations by updating existing cataloged source information with new data from the same sky region as they become available. This process sometimes leads to relatively straightforward conclusions, such as when single sources from two observations are similar in size and position. Other observation results require more logic to combine, such as one observation finding a single, large source and another identifying multiple, smaller sources at the same position. We present examples of different overlapping source detections processed in the current version of the CSC master source pipeline. We explain how they are resolved into entries in the master source database, and examine the challenges of computing source properties for the same source detected multiple times. Future enhancements are also discussed. This work is supported by NASA contract NAS8-03060 (CXC).

  12. Molecular computing origins and promises

    CERN Document Server

    Rambidi, Nicholas G

    2014-01-01

    Molecular Computing explores whether molecular primitives can prove to be real alternatives to contemporary semiconductor means. The text discusses molecular primitives and circuitry for information processing devices.

  13. Microporous and meso porous molecular sieves

    International Nuclear Information System (INIS)

    Araujo, Antonio Souza de

    1999-01-01

    In this work, general aspects on the microporous and mesoporous molecular sieves using inorganic sources of aluminium, silicon, phosphorous, water and structural organic templates are reviewed. The nomenclature, synthesis, structure, acidity and chemical functionality of microporous zeolites and silico alumino phosphate, besides mesoporous MCM-41 material, will be emphasized. (author)

  14. HIERARCHICAL FRAGMENTATION OF THE ORION MOLECULAR FILAMENTS

    International Nuclear Information System (INIS)

    Takahashi, Satoko; Ho, Paul T. P.; Su, Yu-Nung; Teixeira, Paula S.; Zapata, Luis A.

    2013-01-01

    We present a high angular resolution map of the 850 μm continuum emission of the Orion Molecular Cloud-3 (OMC 3) obtained with the Submillimeter Array (SMA); the map is a mosaic of 85 pointings covering an approximate area of 6.'5 × 2.'0 (0.88 × 0.27 pc). We detect 12 spatially resolved continuum sources, each with an H 2 mass between 0.3-5.7 M ☉ and a projected source size between 1400-8200 AU. All the detected sources are on the filamentary main ridge (n H 2 ≥10 6 cm –3 ), and analysis based on the Jeans theorem suggests that they are most likely gravitationally unstable. Comparison of multi-wavelength data sets indicates that of the continuum sources, 6/12 (50%) are associated with molecular outflows, 8/12 (67%) are associated with infrared sources, and 3/12 (25%) are associated with ionized jets. The evolutionary status of these sources ranges from prestellar cores to protostar phase, confirming that OMC-3 is an active region with ongoing embedded star formation. We detect quasi-periodical separations between the OMC-3 sources of ≈17''/0.035 pc. This spatial distribution is part of a large hierarchical structure that also includes fragmentation scales of giant molecular cloud (≈35 pc), large-scale clumps (≈1.3 pc), and small-scale clumps (≈0.3 pc), suggesting that hierarchical fragmentation operates within the Orion A molecular cloud. The fragmentation spacings are roughly consistent with the thermal fragmentation length in large-scale clumps, while for small-scale cores it is smaller than the local fragmentation length. These smaller spacings observed with the SMA can be explained by either a helical magnetic field, cloud rotation, or/and global filament collapse. Finally, possible evidence for sequential fragmentation is suggested in the northern part of the OMC-3 filament.

  15. Molecular outflows in the L1641 region of Orion

    International Nuclear Information System (INIS)

    Morgan, J.A.

    1990-01-01

    Little is known about the interaction between molecular outflows associated with young stellar objects and the parent molecular cloud that produced them. This is because molecular outflows are a recently discovered phenomenon and, so, have not had their global properties studied in great detail and molecular clouds were not mapped to sufficiently high spatial resolution to resolve the interaction. The interaction between molecular outflows and the L1641 molecular cloud is addressed by both identifying and mapping all the molecular outflows as well as the detailed structure of the cloud. Candidate molecular outflows were found from single point 12-CO observations of young stellar objects identified from the IRAS survey data. The candidate sources were then mapped to confirm their molecular outflow nature. From these maps, molecular outflow characteristics such as their morphology, orientation, and energetics were determined. In addition, the Orion molecular cloud was mapped to compare directly with the molecular outflows. The molecular outflows identified were found to have rising infrared spectra, radio continuum emission that suggests a stellar wind or optically thick H II region, and molecular line strengths that indicate that they are embedded within a very dense environment. The lack of an optical counterpart for many molecular outflows suggests that they occur at the earliest stages of stellar evolution. The lack of an optical counterpart for many molecular outflows suggest that they occur at the earliest stages of stellar evolution. The orientations of the molecular outflows appear to lie in no preferred direction and they have shapes that indicate that the molecular cloud is responsible for determining their direction and collimation

  16. Molecular similarity measures.

    Science.gov (United States)

    Maggiora, Gerald M; Shanmugasundaram, Veerabahu

    2011-01-01

    Molecular similarity is a pervasive concept in chemistry. It is essential to many aspects of chemical reasoning and analysis and is perhaps the fundamental assumption underlying medicinal chemistry. Dissimilarity, the complement of similarity, also plays a major role in a growing number of applications of molecular diversity in combinatorial chemistry, high-throughput screening, and related fields. How molecular information is represented, called the representation problem, is important to the type of molecular similarity analysis (MSA) that can be carried out in any given situation. In this work, four types of mathematical structure are used to represent molecular information: sets, graphs, vectors, and functions. Molecular similarity is a pairwise relationship that induces structure into sets of molecules, giving rise to the concept of chemical space. Although all three concepts - molecular similarity, molecular representation, and chemical space - are treated in this chapter, the emphasis is on molecular similarity measures. Similarity measures, also called similarity coefficients or indices, are functions that map pairs of compatible molecular representations that are of the same mathematical form into real numbers usually, but not always, lying on the unit interval. This chapter presents a somewhat pedagogical discussion of many types of molecular similarity measures, their strengths and limitations, and their relationship to one another. An expanded account of the material on chemical spaces presented in the first edition of this book is also provided. It includes a discussion of the topography of activity landscapes and the role that activity cliffs in these landscapes play in structure-activity studies.

  17. Molecular techniques: An overview of methods for the detection of ...

    African Journals Online (AJOL)

    Several DNA molecular markers are now available for use in surveillance and investigation of food-borne outbreaks that were previously difficult to detect. The results from several sources of literature indicate substantially different degrees of sensitivities between conventional detection methods and molecular-based ...

  18. Cell_motility: a cross-platform, open source application for the study of cell motion paths

    Directory of Open Access Journals (Sweden)

    Gevaert Kris

    2006-06-01

    Full Text Available Abstract Background Migration is an important aspect of cellular behaviour and is therefore widely studied in cell biology. Numerous components are known to participate in this process in a highly dynamic manner. In order to obtain a better insight in cell migration, mutants or drugs are used and their motive phenotype is then linked with the disturbing factors. One of the typical approaches to study motion paths of individual cells relies on fitting mean square displacements to a persistent random walk function. Since the numerous calculations involved often rely on diverse commercial software packages, the analysis can be expensive, labour-intensive and error-prone work. Additionally, due to the nature of algorithms employed the calculations involved are not readily reproducible without access to the exact software package(s used. Results We here present the cell_motility software, an open source Java application under the GNU-GPL license that provides a clear and concise analysis workbench for large amounts of cell motion data. Apart from performing the necessary calculations, the software also visualizes the original motion paths as well as the results of the calculations to help the user interpret the data. The application features an intuitive graphical user interface as well as full user and developer documentation and both source and binary files can be freely downloaded from the project website at http://genesis.UGent.be/cell_motility . Conclusion In providing a free, open source software solution for the automated processing of cell motion data, we aim to achieve two important goals: labs can greatly simplify their data analysis pipeline as switching between different computational software packages becomes obsolete (thus reducing the chances for human error during data manipulation and transfer and secondly, to provide scientists in the field with a freely available common platform to perform their analyses, enabling more efficient

  19. Molecular markers for use in plant molecular breeding and germplasm evaluation

    International Nuclear Information System (INIS)

    Edwards, J.D.; McCouch, S.R.

    2007-01-01

    A number of molecular marker technologies exist, each with different advantages and disadvantages. When available, genome sequence allows for the development of greater numbers and higher quality molecular markers. When genome sequence is limited in the organism of interest, related species may serve as sources of molecular markers. Some molecular marker technologies combine the discovery and assay of DNA sequence variations, and therefore can be used in species without the need for prior sequence information and up-front investment in marker development. As a prerequisite for marker-assisted selection (MAS), there must be a known association between genetic markers and genes affecting the phenotype to be modified. Comparative databases can facilitate the transfer of knowledge of genetic marker-phenotype association across species so that discoveries in one species may be applied to many others. Further genomics research and reductions in the costs associated with molecular markers will continue to provide new opportunities to employ MAS. (author)

  20. The Medical Imaging Interaction Toolkit: challenges and advances : 10 years of open-source development.

    Science.gov (United States)

    Nolden, Marco; Zelzer, Sascha; Seitel, Alexander; Wald, Diana; Müller, Michael; Franz, Alfred M; Maleike, Daniel; Fangerau, Markus; Baumhauer, Matthias; Maier-Hein, Lena; Maier-Hein, Klaus H; Meinzer, Hans-Peter; Wolf, Ivo

    2013-07-01

    The Medical Imaging Interaction Toolkit (MITK) has been available as open-source software for almost 10 years now. In this period the requirements of software systems in the medical image processing domain have become increasingly complex. The aim of this paper is to show how MITK evolved into a software system that is able to cover all steps of a clinical workflow including data retrieval, image analysis, diagnosis, treatment planning, intervention support, and treatment control. MITK provides modularization and extensibility on different levels. In addition to the original toolkit, a module system, micro services for small, system-wide features, a service-oriented architecture based on the Open Services Gateway initiative (OSGi) standard, and an extensible and configurable application framework allow MITK to be used, extended and deployed as needed. A refined software process was implemented to deliver high-quality software, ease the fulfillment of regulatory requirements, and enable teamwork in mixed-competence teams. MITK has been applied by a worldwide community and integrated into a variety of solutions, either at the toolkit level or as an application framework with custom extensions. The MITK Workbench has been released as a highly extensible and customizable end-user application. Optional support for tool tracking, image-guided therapy, diffusion imaging as well as various external packages (e.g. CTK, DCMTK, OpenCV, SOFA, Python) is available. MITK has also been used in several FDA/CE-certified applications, which demonstrates the high-quality software and rigorous development process. MITK provides a versatile platform with a high degree of modularization and interoperability and is well suited to meet the challenging tasks of today's and tomorrow's clinically motivated research.

  1. Russian Virtual Observatory: Data Sources

    Directory of Open Access Journals (Sweden)

    Malkov O.

    2016-03-01

    Full Text Available The purpose of this review is to analyze main directions of creation and functioning of major data sources developed by Russian astronomers or with their participation and to compare them with the worldwide trends in these fields. We discuss astronomical space missions of the past, present, and future (Astron, INTEGRAL, WSO-UV, Spectrum Roentgen Gamma, Lyra-B, high-quality photometric atlases and catalogues, and spectroscopic data sources, primarily VALD and the global VAMDC framework for the maintenance and distribution of atomic and molecular data. We describe collection, analysis, and dissemination of astronomical data on minor bodies of the Solar System and on variable stars. Also described is the project joining data for all observational types of binary and multiple stars, Binary star DataBase (BDB.

  2. A double-stage pulsed discharge fluorine atom beam source

    International Nuclear Information System (INIS)

    Ren Zefeng; Qiu Minghui; Che Li; Dai Dongxu; Wang Xiuyan; Yang Xueming

    2006-01-01

    Molecular-beam intensity and speed ratio are two major limiting factors in many molecular-beam experiments. This article reports a high-intensity, high-speed-ratio, pulsed supersonic fluorine atom beam source using a double-stage discharge beam source. Its performance is indicated by the high-resolution time-of-flight spectrum in the crossed beam experiment of F( 2 P)+para-H 2

  3. New sources and instrumentation for neutrons in biology

    DEFF Research Database (Denmark)

    Teixeira, S. C. M.; Zaccai, G.; Ankner, J.

    2008-01-01

    Neutron radiation offers significant advantages for the study of biological molecular structure and dynamics. A broad and significant effort towards instrumental and methodological development to facilitate biology experiments at neutron sources worldwide is reviewed.......Neutron radiation offers significant advantages for the study of biological molecular structure and dynamics. A broad and significant effort towards instrumental and methodological development to facilitate biology experiments at neutron sources worldwide is reviewed....

  4. A new storage-ring light source

    Energy Technology Data Exchange (ETDEWEB)

    Chao, Alex [SLAC National Accelerator Lab., Menlo Park, CA (United States)

    2015-06-01

    A recently proposed technique in storage ring accelerators is applied to provide potential high-power sources of photon radiation. The technique is based on the steady-state microbunching (SSMB) mechanism. As examples of this application, one may consider a high-power DUV photon source for research in atomic and molecular physics or a high-power EUV radiation source for industrial lithography. A less challenging proof-of-principle test to produce IR radiation using an existing storage ring is also considered.

  5. Contributions to advances in blend pellet products (BPP) research on molecular structure and molecular nutrition interaction by advanced synchrotron and globar molecular (Micro)spectroscopy.

    Science.gov (United States)

    Guevara-Oquendo, Víctor H; Zhang, Huihua; Yu, Peiqiang

    2018-04-13

    To date, advanced synchrotron-based and globar-sourced techniques are almost unknown to food and feed scientists. There has been little application of these advanced techniques to study blend pellet products at a molecular level. This article aims to provide recent research on advanced synchrotron and globar vibrational molecular spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction. How processing induced molecular structure changes in relation to nutrient availability and utilization of the blend pellet products. The study reviews Utilization of co-product components for blend pellet product in North America; Utilization and benefits of inclusion of pulse screenings; Utilization of additives in blend pellet products; Application of pellet processing in blend pellet products; Conventional evaluation techniques and methods for blend pellet products. The study focus on recent applications of cutting-edge vibrational molecular spectroscopy for molecular structure and molecular structure association with nutrient utilization in blend pellet products. The information described in this article gives better insight on how advanced molecular (micro)spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction.

  6. The use of molecular chemistry (pyrolysis-GC/MS) in the environmental interpretation of peat

    NARCIS (Netherlands)

    Schellekens, J.

    2013-01-01

      The molecular composition of organic matter in peatlands reflects local conditions and stores information about botanical composition (plant source) as well as the degree of and conditions during decomposition. A reliable hydrological (and hence palaeoclimatological) interpretation of source

  7. EAACI Molecular Allergology User's Guide.

    Science.gov (United States)

    Matricardi, P M; Kleine-Tebbe, J; Hoffmann, H J; Valenta, R; Hilger, C; Hofmaier, S; Aalberse, R C; Agache, I; Asero, R; Ballmer-Weber, B; Barber, D; Beyer, K; Biedermann, T; Bilò, M B; Blank, S; Bohle, B; Bosshard, P P; Breiteneder, H; Brough, H A; Caraballo, L; Caubet, J C; Crameri, R; Davies, J M; Douladiris, N; Ebisawa, M; EIgenmann, P A; Fernandez-Rivas, M; Ferreira, F; Gadermaier, G; Glatz, M; Hamilton, R G; Hawranek, T; Hellings, P; Hoffmann-Sommergruber, K; Jakob, T; Jappe, U; Jutel, M; Kamath, S D; Knol, E F; Korosec, P; Kuehn, A; Lack, G; Lopata, A L; Mäkelä, M; Morisset, M; Niederberger, V; Nowak-Węgrzyn, A H; Papadopoulos, N G; Pastorello, E A; Pauli, G; Platts-Mills, T; Posa, D; Poulsen, L K; Raulf, M; Sastre, J; Scala, E; Schmid, J M; Schmid-Grendelmeier, P; van Hage, M; van Ree, R; Vieths, S; Weber, R; Wickman, M; Muraro, A; Ollert, M

    2016-05-01

    The availability of allergen molecules ('components') from several protein families has advanced our understanding of immunoglobulin E (IgE)-mediated responses and enabled 'component-resolved diagnosis' (CRD). The European Academy of Allergy and Clinical Immunology (EAACI) Molecular Allergology User's Guide (MAUG) provides comprehensive information on important allergens and describes the diagnostic options using CRD. Part A of the EAACI MAUG introduces allergen molecules, families, composition of extracts, databases, and diagnostic IgE, skin, and basophil tests. Singleplex and multiplex IgE assays with components improve both sensitivity for low-abundance allergens and analytical specificity; IgE to individual allergens can yield information on clinical risks and distinguish cross-reactivity from true primary sensitization. Part B discusses the clinical and molecular aspects of IgE-mediated allergies to foods (including nuts, seeds, legumes, fruits, vegetables, cereal grains, milk, egg, meat, fish, and shellfish), inhalants (pollen, mold spores, mites, and animal dander), and Hymenoptera venom. Diagnostic algorithms and short case histories provide useful information for the clinical workup of allergic individuals targeted for CRD. Part C covers protein families containing ubiquitous, highly cross-reactive panallergens from plant (lipid transfer proteins, polcalcins, PR-10, profilins) and animal sources (lipocalins, parvalbumins, serum albumins, tropomyosins) and explains their diagnostic and clinical utility. Part D lists 100 important allergen molecules. In conclusion, IgE-mediated reactions and allergic diseases, including allergic rhinoconjunctivitis, asthma, food reactions, and insect sting reactions, are discussed from a novel molecular perspective. The EAACI MAUG documents the rapid progression of molecular allergology from basic research to its integration into clinical practice, a quantum leap in the management of allergic patients. © 2016 John Wiley

  8. Sources of polarized neutrons

    International Nuclear Information System (INIS)

    Walter, L.

    1983-01-01

    Various sources of polarized neutrons are reviewed. Monoenergetic source produced with unpolarized or polarized beams, white sources of polarized neutrons, production by transmissions through polarized hydrogen targets and polarized thermal neutronsare discussed, with appropriate applications included. (U.K.)

  9. Pacemakers lower sources

    International Nuclear Information System (INIS)

    Greatbatch, W.

    1984-01-01

    Energy sources for cardiac facing are considered including radioisotope sources, in a broad conceptual and historical framework.The main guidelines for future development of energy sources are assessed

  10. Molecular photoionization dynamics

    International Nuclear Information System (INIS)

    Dehmer, J.L.

    1982-01-01

    This program seeks to develop both physical insight and quantitative characterization of molecular photoionization processes. Progress is briefly described, and some publications resulting from the research are listed

  11. Polymer friction Molecular Dynamics

    DEFF Research Database (Denmark)

    Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.

    We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....

  12. GRASS GIS: The first Open Source Temporal GIS

    Science.gov (United States)

    Gebbert, Sören; Leppelt, Thomas

    2015-04-01

    over temporal aggregation, temporal accumulation, spatio-temporal statistics, spatio-temporal sampling, temporal algebra, temporal topology analysis, time series animation and temporal topology visualization to time series import and export capabilities with support for NetCDF and VTK data formats. We will present several temporal modules that support parallel processing of raster and 3D raster time series. [1] GRASS GIS Open Source Approaches in Spatial Data Handling In Open Source Approaches in Spatial Data Handling, Vol. 2 (2008), pp. 171-199, doi:10.1007/978-3-540-74831-19 by M. Neteler, D. Beaudette, P. Cavallini, L. Lami, J. Cepicky edited by G. Brent Hall, Michael G. Leahy [2] Gebbert, S., Pebesma, E., 2014. A temporal GIS for field based environmental modeling. Environ. Model. Softw. 53, 1-12. [3] Zambelli, P., Gebbert, S., Ciolli, M., 2013. Pygrass: An Object Oriented Python Application Programming Interface (API) for Geographic Resources Analysis Support System (GRASS) Geographic Information System (GIS). ISPRS Intl Journal of Geo-Information 2, 201-219. [4] Löwe, P., Klump, J., Thaler, J. (2012): The FOSS GIS Workbench on the GFZ Load Sharing Facility compute cluster, (Geophysical Research Abstracts Vol. 14, EGU2012-4491, 2012), General Assembly European Geosciences Union (Vienna, Austria 2012). [5] Akhter, S., Aida, K., Chemin, Y., 2010. "GRASS GIS on High Performance Computing with MPI, OpenMP and Ninf-G Programming Framework". ISPRS Conference, Kyoto, 9-12 August 2010

  13. 1985 bibliography of atomic and molecular processes

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.; Griffin, P.M.; Havener, C.C.; Howald, A.M.; Kirkpatrick, M.I.; McDaniel, E.W.; Meyer, F.W.; Morgan, T.J. (comps.)

    1986-06-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1985. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  14. Molecular-beam spectroscopy of interhalogen molecules

    International Nuclear Information System (INIS)

    Sherrow, S.A.

    1983-08-01

    A molecular-beam electric-resonance spectrometer employing a supersonic nozzle source has been used to obtain hyperfine spectra of 79 Br 35 Cl. Analyses of these spectra and of microwave spectra published by other authors have yielded new values for the electric dipole moment and for the nuclear quadrupole coupling constants in this molecule. The new constants are significantly different from the currently accepted values. Van der Waals clusters containing chlorine monofluoride have been studied under various expansion conditions by the molecular-beam electric-deflection method. The structural possibilities indicated by the results are discussed, and cluster geometries are proposed

  15. 1984 Bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.

    1985-04-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1984. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  16. Bibliography of atomic and molecular processes, 1983

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Gregory, D.C.; Kirkpatrick, M.I.; McDaniel, E.W.; McKnight, R.H.; Meyer, F.W.; Morgan, T.J.; Phaneuf, R.A. (comps.)

    1984-10-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1983. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  17. Bibliography of atomic and molecular processes, 1983

    International Nuclear Information System (INIS)

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.

    1984-10-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1983. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  18. 1982 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.

    1984-05-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1982. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  19. 1985 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    Barnett, C.F.; Gilbody, H.B.; Gregory, D.C.

    1986-06-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1985. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory

  20. 1978 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    1980-03-01

    This annotated bibliography lists 2557 works on atomic and molecular processes reported in publications dated 1978. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors

  1. 1982 bibliography of atomic and molecular processes

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, C.F.; Crandall, D.H.; Gilbody, H.B.; Gregory, D.C.; Kirkpatrick, M.I.; McDaniel, E.W.; McKnight, R.H.; Meyer, F.W.; Morgan, T.J.; Phaneuf, R.A. (comps.)

    1984-05-01

    This annotated bibliography includes papers on atomic and molecular processes published during 1982. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing, the entries are indexed according to the categories and according to reactants within each subcategory.

  2. Physics with fast molecular-ion beams

    International Nuclear Information System (INIS)

    Kanter, E.P.

    1980-01-01

    Fast (MeV) molecular-ion beams provide a unique source of energetic projectile nuclei which are correlated in space and time. The recognition of this property has prompted several recent investigations of various aspects of the interactions of these ions with matter. High-resolution measurements on the fragments resulting from these interactions have already yielded a wealth of new information on such diverse topics as plasma oscillations in solids and stereochemical structures of molecular ions as well as a variety of atomic collision phenomena. The general features of several such experiments will be discussed and recent results will be presented

  3. 1979 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    1980-08-01

    This annotated bibliography lists 2146 works on atomic and molecular processes reported in publications dated 1979. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors

  4. 1980 bibliography of atomic and molecular processes

    International Nuclear Information System (INIS)

    1982-02-01

    This annotated bibliography lists 2866 works on atomic and molecular processes reported in publications dated 1980. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors

  5. Sources management; La gestion des sources

    Energy Technology Data Exchange (ETDEWEB)

    Mansoux, H.; Gourmelon; Scanff, P.; Fournet, F. [Institut de Radioprotection et de Surete Nucleaire, 92 - Fontenay-aux-Roses (France); Murith, Ch. [Office Federal de la SantePublique (Switzerland); Saint-Paul, N. [NOVAR, 75 - Paris (France); Colson, P. [Electricite de France (EDF/DPN), 93 - Saint-Denis (France); Jouve, A.; Feron, F. [Direction Generale de al Surete Nucleaire et de la Radioprotection, 75 - Paris (France); Haranger, D. [Electricite de France (EDF), 75 - Paris (France); Mathieu, P. [Institut Pasteur, 75 - Paris (France); Paycha, F. [CHU Louis Mourier, Unitede Medecine Nucleaire Assistance Publique-Hopitaux de Paris, 92 - Colombes (France); Israel, S. [CEGELEC NDT et la gestion des sources radioactives (France); Auboiroux, B. [APAVE (France); Chartier, P. [DRIRE de Basse-Normandie, Div. Surete Nucleaire et Radioprotection, 14 - Caen (France)

    2005-07-01

    Organized by the section of technical protection of the French society of radiation protection ( S.F.R.P.), these two days had for objective to review the evolution of the rule relative to the sources of ionising radiations 'sealed and unsealed radioactive sources, electric generators'. They addressed all the actors concerned by the implementation of the new regulatory system in the different sectors of activities ( research, medicine and industry): Authorities, manufacturers, and suppliers of sources, holders and users, bodies involved in the approval of sources, carriers. (N.C.)

  6. Making molecular machines work

    NARCIS (Netherlands)

    Browne, Wesley R.; Feringa, Ben L.

    2006-01-01

    In this review we chart recent advances in what is at once an old and very new field of endeavour the achievement of control of motion at the molecular level including solid-state and surface-mounted rotors, and its natural progression to the development of synthetic molecular machines. Besides a

  7. Veterinary Molecular Diagnostics

    NARCIS (Netherlands)

    Roest, H.I.J.; Engelsma, M.Y.; Weesendorp, E.; Bossers, A.; Elbers, A.R.W.

    2017-01-01

    In veterinary molecular diagnostics, samples originating from animals are tested. Developments in the farm animals sector and in our societal attitude towards pet animals have resulted in an increased demand for fast and reliable diagnostic techniques. Molecular diagnostics perfectly matches this

  8. Molecular Beacons in Diagnostics

    OpenAIRE

    Tyagi, Sanjay; Kramer, Fred Russell

    2012-01-01

    Recent technical advances have begun to realize the potential of molecular beacons to test for diverse infections in clinical diagnostic laboratories. These include the ability to test for, and quantify, multiple pathogens in the same clinical sample, and to detect antibiotic resistant strains within hours. The design principles of molecular beacons have also spawned a variety of allied technologies.

  9. Molecular microbial ecology manual

    NARCIS (Netherlands)

    Kowalchuk, G.A.; Bruijn, de F.J.; Head, I.M.; Akkermans, A.D.L.

    2004-01-01

    The field of microbial ecology has been revolutionized in the past two decades by the introduction of molecular methods into the toolbox of the microbial ecologist. This molecular arsenal has helped to unveil the enormity of microbial diversity across the breadth of the earth's ecosystems, and has

  10. Principles of molecular oncology

    National Research Council Canada - National Science Library

    Bronchud, Miguel H

    2008-01-01

    ...-threatening diseases. Many new molecularly targeted diagnostics and therapeutics described in this text, developed based on the rapid growth in our understanding of the molecular basis of cancer, already substantially improve survival of patients with previously lethal malignancies, and also improve quality of life because of fewer toxicities. Clearly re...

  11. Molecular Typing and Differentiation

    Science.gov (United States)

    In this chapter, general background and bench protocols are provided for a number of molecular typing techniques in common use today. Methods for the molecular typing and differentiation of microorganisms began to be widely adopted following the development of the polymerase chai...

  12. Principles of molecular oncology

    National Research Council Canada - National Science Library

    Bronchud, Miguel H; Thomas, E. Donnall; Weatherall, D. J; Crowther, D. G

    2004-01-01

    ...-threatening diseases. Many new molecularly targeted diagnostics and therapeutics described in this text, developed based on the rapid growth in our understanding of the molecular basis of cancer, already substantially improve survival of patients with previously lethal malignancies, and also improve quality of life because of fewer toxicities. Clearly re...

  13. Ionic and Molecular Liquids

    DEFF Research Database (Denmark)

    Chaban, Vitaly V.; Prezhdo, Oleg

    2013-01-01

    applications of RTILs in combination with molecular liquids, concentrating on three significant areas: (1) the use of molecular liquids to decrease the viscosity of RTILs; (2) the role of RTIL micelle formation in water and organic solvents; and (3) the ability of RTILs to adsorb pollutant gases. Current...

  14. Molecular Stirrers in Action

    NARCIS (Netherlands)

    Chen, Jiawen; Kistemaker, Jos C. M.; Robertus, Jort; Feringa, Ben L.

    2014-01-01

    A series of first-generation light-driven molecular motors with rigid substituents of varying length was synthesized to act as "molecular stirrers". Their rotary motion was studied by H-1 NMR and UV-vis absorption spectroscopy in a variety of solvents with different polarity and viscosity.

  15. Molecular subgroups of medulloblastoma

    OpenAIRE

    Northcott, Paul A; Dubuc, Adrian M; Pfister, Stefan; Taylor, Michael D

    2012-01-01

    Recent efforts at stratifying medulloblastomas based on their molecular features have revolutionized our understanding of this morbidity. Collective efforts by multiple independent groups have subdivided medulloblastoma from a single disease into four distinct molecular subgroups characterized by disparate transcriptional signatures, mutational spectra, copy number profiles and, most importantly, clinical features. We present a summary of recent studies that have contributed to our understand...

  16. Theoretical molecular biophysics

    CERN Document Server

    Scherer, Philipp O J

    2017-01-01

    This book gives an introduction to molecular biophysics. It starts from material properties at equilibrium related to polymers, dielectrics and membranes. Electronic spectra are developed for the understanding of elementary dynamic processes in photosynthesis including proton transfer and dynamics of molecular motors. Since the molecular structures of functional groups of bio-systems were resolved, it has become feasible to develop a theory based on the quantum theory and statistical physics with emphasis on the specifics of the high complexity of bio-systems. This introduction to molecular aspects of the field focuses on solvable models. Elementary biological processes provide as special challenge the presence of partial disorder in the structure which does not destroy the basic reproducibility of the processes. Apparently the elementary molecular processes are organized in a way to optimize the efficiency. Learning from nature by means exploring the relation between structure and function may even help to b...

  17. Molecular Population Genetics.

    Science.gov (United States)

    Casillas, Sònia; Barbadilla, Antonio

    2017-03-01

    Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. Copyright © 2017 Casillas and Barbadilla.

  18. EDITORIAL: Molecular Imaging Technology

    Science.gov (United States)

    Asai, Keisuke; Okamoto, Koji

    2006-06-01

    'Molecular Imaging Technology' focuses on image-based techniques using nanoscale molecules as sensor probes to measure spatial variations of various species (molecular oxygen, singlet oxygen, carbon dioxide, nitric monoxide, etc) and physical properties (pressure, temperature, skin friction, velocity, mechanical stress, etc). This special feature, starting on page 1237, contains selected papers from The International Workshop on Molecular Imaging for Interdisciplinary Research, sponsored by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) in Japan, which was held at the Sendai Mediatheque, Sendai, Japan, on 8 9 November 2004. The workshop was held as a sequel to the MOSAIC International Workshop that was held in Tokyo in 2003, to summarize the outcome of the 'MOSAIC Project', a five-year interdisciplinary project supported by Techno-Infrastructure Program, the Special Coordination Fund for Promotion of Science Technology to develop molecular sensor technology for aero-thermodynamic research. The workshop focused on molecular imaging technology and its applications to interdisciplinary research areas. More than 110 people attended this workshop from various research fields such as aerospace engineering, automotive engineering, radiotechnology, fluid dynamics, bio-science/engineering and medical engineering. The purpose of this workshop is to stimulate intermixing of these interdisciplinary fields for further development of molecular sensor and imaging technology. It is our pleasure to publish the seven papers selected from our workshop as a special feature in Measurement and Science Technology. We will be happy if this issue inspires people to explore the future direction of molecular imaging technology for interdisciplinary research.

  19. Molecularly Imprinted Membranes

    Science.gov (United States)

    Trotta, Francesco; Biasizzo, Miriam; Caldera, Fabrizio

    2012-01-01

    Although the roots of molecularly imprinted polymers lie in the beginning of 1930s in the past century, they have had an exponential growth only 40–50 years later by the works of Wulff and especially by Mosbach. More recently, it was also proved that molecular imprinted membranes (i.e., polymer thin films) that show recognition properties at molecular level of the template molecule are used in their formation. Different procedures and potential application in separation processes and catalysis are reported. The influences of different parameters on the discrimination abilities are also discussed. PMID:24958291

  20. Photoionization and molecular structure

    International Nuclear Information System (INIS)

    Palma, A.

    1983-01-01

    A presentation is here given of the theoretical work on photoionization and molecular structure carried out by the author and coworkers. The implications of the photoionization process on the molecular geometry are emphasized. In particular, the ionization effect on deep orbitals is considered and it is shown that, contrary to traditional thinking, these orbitals have relevant effects on the molecular geometry. The problem of calculating photoionization relative intensities for the full spectrum is also considered, and the results of the present model are compared with experimental and other theoretical results. (author)

  1. The Chandra Source Catalog: Source Variability

    Science.gov (United States)

    Nowak, Michael; Rots, A. H.; McCollough, M. L.; Primini, F. A.; Glotfelty, K. J.; Bonaventura, N. R.; Chen, J. C.; Davis, J. E.; Doe, S. M.; Evans, J. D.; Evans, I.; Fabbiano, G.; Galle, E. C.; Gibbs, D. G., II; Grier, J. D.; Hain, R.; Hall, D. M.; Harbo, P. N.; He, X.; Houck, J. C.; Karovska, M.; Lauer, J.; McDowell, J. C.; Miller, J. B.; Mitschang, A. W.; Morgan, D. L.; Nichols, J. S.; Plummer, D. A.; Refsdal, B. L.; Siemiginowska, A. L.; Sundheim, B. A.; Tibbetts, M. S.; van Stone, D. W.; Winkelman, S. L.; Zografou, P.

    2009-09-01

    The Chandra Source Catalog (CSC) contains fields of view that have been studied with individual, uninterrupted observations that span integration times ranging from 1 ksec to 160 ksec, and a large number of which have received (multiple) repeat observations days to years later. The CSC thus offers an unprecedented look at the variability of the X-ray sky over a broad range of time scales, and across a wide diversity of variable X-ray sources: stars in the local galactic neighborhood, galactic and extragalactic X-ray binaries, Active Galactic Nuclei, etc. Here we describe the methods used to identify and quantify source variability within a single observation, and the methods used to assess the variability of a source when detected in multiple, individual observations. Three tests are used to detect source variability within a single observation: the Kolmogorov-Smirnov test and its variant, the Kuiper test, and a Bayesian approach originally suggested by Gregory and Loredo. The latter test not only provides an indicator of variability, but is also used to create a best estimate of the variable lightcurve shape. We assess the performance of these tests via simulation of statistically stationary, variable processes with arbitrary input power spectral densities (here we concentrate on results of red noise simulations) at variety of mean count rates and fractional root mean square variabilities relevant to CSC sources. We also assess the false positive rate via simulations of constant sources whose sole source of fluctuation is Poisson noise. We compare these simulations to an assessment of the variability found in real CSC sources, and estimate the variability sensitivities of the CSC.

  2. A Molecular Description of Cellulose Biosynthesis

    Science.gov (United States)

    McNamara, Joshua T.; Morgan, Jacob L.W.; Zimmer, Jochen

    2016-01-01

    Cellulose is the most abundant biopolymer on Earth, and certain organisms from bacteria to plants and animals synthesize cellulose as an extracellular polymer for various biological functions. Humans have used cellulose for millennia as a material and an energy source, and the advent of a lignocellulosic fuel industry will elevate it to the primary carbon source for the burgeoning renewable energy sector. Despite the biological and societal importance of cellulose, the molecular mechanism by which it is synthesized is now only beginning to emerge. On the basis of recent advances in structural and molecular biology on bacterial cellulose synthases, we review emerging concepts of how the enzymes polymerize glucose molecules, how the nascent polymer is transported across the plasma membrane, and how bacterial cellulose biosynthesis is regulated during biofilm formation. Additionally, we review evolutionary commonalities and differences between cellulose synthases that modulate the nature of the cellulose product formed. PMID:26034894

  3. Molecular beam epitaxy for the future

    International Nuclear Information System (INIS)

    Takahashi, K.

    1984-01-01

    Molecular beam epitaxy (MBE) is most commonly used to fabricate super-lattices, high electron mobility transistors, multi-quantum well lasers and other new semiconductor devices by utilizing its excellent controlability. MBE for the future is presumed to include techniques such as metalorganic chemical vapor deposition, photochemical reaction process using gas sources and ion implantation. A report on the crystal growth of GaAs using metalorganics, trimethylgallium and triethylgallium, which are usually used in chemical vapor deposition, as gaseous sources of gallium in an MBE system is made. (Author) [pt

  4. THE CHANDRA SOURCE CATALOG

    International Nuclear Information System (INIS)

    Evans, Ian N.; Primini, Francis A.; Glotfelty, Kenny J.; Anderson, Craig S.; Bonaventura, Nina R.; Chen, Judy C.; Doe, Stephen M.; Evans, Janet D.; Fabbiano, Giuseppina; Galle, Elizabeth C.; Gibbs, Danny G.; Grier, John D.; Hain, Roger M.; Harbo, Peter N.; He Xiangqun; Karovska, Margarita; Kashyap, Vinay L.; Davis, John E.; Houck, John C.; Hall, Diane M.

    2010-01-01

    The Chandra Source Catalog (CSC) is a general purpose virtual X-ray astrophysics facility that provides access to a carefully selected set of generally useful quantities for individual X-ray sources, and is designed to satisfy the needs of a broad-based group of scientists, including those who may be less familiar with astronomical data analysis in the X-ray regime. The first release of the CSC includes information about 94,676 distinct X-ray sources detected in a subset of public Advanced CCD Imaging Spectrometer imaging observations from roughly the first eight years of the Chandra mission. This release of the catalog includes point and compact sources with observed spatial extents ∼<30''. The catalog (1) provides access to the best estimates of the X-ray source properties for detected sources, with good scientific fidelity, and directly supports scientific analysis using the individual source data; (2) facilitates analysis of a wide range of statistical properties for classes of X-ray sources; and (3) provides efficient access to calibrated observational data and ancillary data products for individual X-ray sources, so that users can perform detailed further analysis using existing tools. The catalog includes real X-ray sources detected with flux estimates that are at least 3 times their estimated 1σ uncertainties in at least one energy band, while maintaining the number of spurious sources at a level of ∼<1 false source per field for a 100 ks observation. For each detected source, the CSC provides commonly tabulated quantities, including source position, extent, multi-band fluxes, hardness ratios, and variability statistics, derived from the observations in which the source is detected. In addition to these traditional catalog elements, for each X-ray source the CSC includes an extensive set of file-based data products that can be manipulated interactively, including source images, event lists, light curves, and spectra from each observation in which a

  5. The Chandra Source Catalog

    Science.gov (United States)

    Evans, Ian N.; Primini, Francis A.; Glotfelty, Kenny J.; Anderson, Craig S.; Bonaventura, Nina R.; Chen, Judy C.; Davis, John E.; Doe, Stephen M.; Evans, Janet D.; Fabbiano, Giuseppina; Galle, Elizabeth C.; Gibbs, Danny G., II; Grier, John D.; Hain, Roger M.; Hall, Diane M.; Harbo, Peter N.; He, Xiangqun Helen; Houck, John C.; Karovska, Margarita; Kashyap, Vinay L.; Lauer, Jennifer; McCollough, Michael L.; McDowell, Jonathan C.; Miller, Joseph B.; Mitschang, Arik W.; Morgan, Douglas L.; Mossman, Amy E.; Nichols, Joy S.; Nowak, Michael A.; Plummer, David A.; Refsdal, Brian L.; Rots, Arnold H.; Siemiginowska, Aneta; Sundheim, Beth A.; Tibbetts, Michael S.; Van Stone, David W.; Winkelman, Sherry L.; Zografou, Panagoula

    2010-07-01

    The Chandra Source Catalog (CSC) is a general purpose virtual X-ray astrophysics facility that provides access to a carefully selected set of generally useful quantities for individual X-ray sources, and is designed to satisfy the needs of a broad-based group of scientists, including those who may be less familiar with astronomical data analysis in the X-ray regime. The first release of the CSC includes information about 94,676 distinct X-ray sources detected in a subset of public Advanced CCD Imaging Spectrometer imaging observations from roughly the first eight years of the Chandra mission. This release of the catalog includes point and compact sources with observed spatial extents lsim30''. The catalog (1) provides access to the best estimates of the X-ray source properties for detected sources, with good scientific fidelity, and directly supports scientific analysis using the individual source data; (2) facilitates analysis of a wide range of statistical properties for classes of X-ray sources; and (3) provides efficient access to calibrated observational data and ancillary data products for individual X-ray sources, so that users can perform detailed further analysis using existing tools. The catalog includes real X-ray sources detected with flux estimates that are at least 3 times their estimated 1σ uncertainties in at least one energy band, while maintaining the number of spurious sources at a level of lsim1 false source per field for a 100 ks observation. For each detected source, the CSC provides commonly tabulated quantities, including source position, extent, multi-band fluxes, hardness ratios, and variability statistics, derived from the observations in which the source is detected. In addition to these traditional catalog elements, for each X-ray source the CSC includes an extensive set of file-based data products that can be manipulated interactively, including source images, event lists, light curves, and spectra from each observation in which a

  6. Molecular hydrogen jets from the Orion nebula

    International Nuclear Information System (INIS)

    Taylor, K.N.R.; Storey, J.W.V.; Zealey, W.J.

    1984-01-01

    In an attempt to understand the relationship of the recently discovered complex of Herbig Haro objects in Orion to the IR sources in this region, the authors have carried out a survey of the molecular hydrogen S(1) line distribution. The observations have led to the discovery of a previously unsuspected structure of finger-like filaments of H 2 emission extending radially outwards from a common centre at IRC9. (author)

  7. Polypeptides Based Molecular Electronics

    National Research Council Canada - National Science Library

    Lam, Yeng M; Mhaisalkar, Subodh; Li, Lain-Jong; Dravid, Vinayak P; Shekhawat, Gajendra S; Suri, Raman

    2008-01-01

    ... the formation of molecular devices such as transistors, diodes, and sensors. We have designed the peptides, arranged them on substrates using self-assembly, Dip-PEN nanolithography, and also e-beam assisted lithography...

  8. Molecular electronic junction transport

    DEFF Research Database (Denmark)

    Solomon, Gemma C.; Herrmann, Carmen; Ratner, Mark

    2012-01-01

    Whenasinglemolecule,oracollectionofmolecules,isplacedbetween two electrodes and voltage is applied, one has a molecular transport junction. We discuss such junctions, their properties, their description, and some of their applications. The discussion is qualitative rather than quantitative, and f...

  9. Atomic and Molecular Interactions

    International Nuclear Information System (INIS)

    2002-01-01

    The Gordon Research Conference (GRC) on Atomic and Molecular Interactions was held at Roger Williams University, Bristol, RI. Emphasis was placed on current unpublished research and discussion of the future target areas in this field

  10. Noncovalent Molecular Electronics.

    Science.gov (United States)

    Gryn'ova, G; Corminboeuf, C

    2018-05-03

    Molecular electronics covers several distinctly different conducting architectures, including organic semiconductors and single-molecule junctions. The noncovalent interactions, abundant in the former, are also often found in the latter, i.e., the dimer junctions. In the present work, we draw the parallel between the two types of noncovalent molecular electronics for a range of π-conjugated heteroaromatic molecules. In silico modeling allows us to distill the factors that arise from the chemical nature of their building blocks and from their mutual arrangement. We find that the same compounds are consistently the worst and the best performers in the two types of electronic assemblies, emphasizing the universal imprint of the underlying chemistry of the molecular cores on their diverse charge transport characteristics. The interplay between molecular and intermolecular factors creates a spectrum of noncovalent conductive architectures, which can be manipulated using the design strategies based upon the established relationships between chemistry and transport.

  11. The Molecular Foundry (TMF)

    Data.gov (United States)

    Federal Laboratory Consortium — Founded in 2006 by the Department of Energy (DOE), the Molecular Foundry is a critical part of the DOE's National Nanotechnology Initiative, a multi-agency framework...

  12. Advanced spallation neutron sources for condensed matter research

    International Nuclear Information System (INIS)

    Lovesey, S.W.; Stirling, G.C.

    1984-03-01

    Advanced spallation neutron sources afford significant advantages over existing high flux reactors. The effective flux is much greater than that currently available with reactor sources. A ten-fold increase in neutron flux will be a major benefit to a wide range of condensed matter studies, and it will realise important experiments that are marginal at reactor sources. Moreover, the high intensity of epithermal neutrons open new vistas in studies of electronic states and molecular vibrations. (author)

  13. Molecular Electronic Shift Registers

    Science.gov (United States)

    Beratan, David N.; Onuchic, Jose N.

    1990-01-01

    Molecular-scale shift registers eventually constructed as parts of high-density integrated memory circuits. In principle, variety of organic molecules makes possible large number of different configurations and modes of operation for such shift-register devices. Several classes of devices and implementations in some specific types of molecules proposed. All based on transfer of electrons or holes along chains of repeating molecular units.

  14. Molecular imaging in oncology

    Energy Technology Data Exchange (ETDEWEB)

    Schober, Otmar; Riemann, Burkhard (eds.) [Universitaetsklinikum Muenster (Germany). Klinik fuer Nuklearmedizin

    2013-02-01

    Considers in detail all aspects of molecular imaging in oncology, ranging from basic research to clinical applications in the era of evidence-based medicine. Examines technological issues and probe design. Discusses preclinical studies in detail, with particular attention to multimodality imaging. Presents current clinical use of PET/CT, SPECT/CT, and optical imagingWritten by acknowledged experts. The impact of molecular imaging on diagnostics, therapy, and follow-up in oncology is increasing significantly. The process of molecular imaging includes key biotarget identification, design of specific molecular imaging probes, and their preclinical evaluation, e.g., in vivo using small animal studies. A multitude of such innovative molecular imaging probes have already entered clinical diagnostics in oncology. There is no doubt that in future the emphasis will be on multimodality imaging in which morphological, functional, and molecular imaging techniques are combined in a single clinical investigation that will optimize diagnostic processes. This handbook addresses all aspects of molecular imaging in oncology, ranging from basic research to clinical applications in the era of evidence-based medicine. The first section is devoted to technology and probe design, and examines a variety of PET and SPECT tracers as well as multimodality probes. Preclinical studies are then discussed in detail, with particular attention to multimodality imaging. In the third section, diverse clinical applications are presented, and the book closes by looking at future challenges. This handbook will be of value to all who are interested in the revolution in diagnostic oncology that is being brought about by molecular imaging.

  15. Human papillomavirus molecular biology.

    Science.gov (United States)

    Harden, Mallory E; Munger, Karl

    Human papillomaviruses are small DNA viruses with a tropism for squamous epithelia. A unique aspect of human papillomavirus molecular biology involves dependence on the differentiation status of the host epithelial cell to complete the viral lifecycle. A small group of these viruses are the etiologic agents of several types of human cancers, including oral and anogenital tract carcinomas. This review focuses on the basic molecular biology of human papillomaviruses. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Molecular imaging in oncology

    International Nuclear Information System (INIS)

    Schober, Otmar; Riemann, Burkhard

    2013-01-01

    Considers in detail all aspects of molecular imaging in oncology, ranging from basic research to clinical applications in the era of evidence-based medicine. Examines technological issues and probe design. Discusses preclinical studies in detail, with particular attention to multimodality imaging. Presents current clinical use of PET/CT, SPECT/CT, and optical imagingWritten by acknowledged experts. The impact of molecular imaging on diagnostics, therapy, and follow-up in oncology is increasing significantly. The process of molecular imaging includes key biotarget identification, design of specific molecular imaging probes, and their preclinical evaluation, e.g., in vivo using small animal studies. A multitude of such innovative molecular imaging probes have already entered clinical diagnostics in oncology. There is no doubt that in future the emphasis will be on multimodality imaging in which morphological, functional, and molecular imaging techniques are combined in a single clinical investigation that will optimize diagnostic processes. This handbook addresses all aspects of molecular imaging in oncology, ranging from basic research to clinical applications in the era of evidence-based medicine. The first section is devoted to technology and probe design, and examines a variety of PET and SPECT tracers as well as multimodality probes. Preclinical studies are then discussed in detail, with particular attention to multimodality imaging. In the third section, diverse clinical applications are presented, and the book closes by looking at future challenges. This handbook will be of value to all who are interested in the revolution in diagnostic oncology that is being brought about by molecular imaging.

  17. Inner Source Pickup Ions Observed by Ulysses

    Science.gov (United States)

    Gloeckler, G.

    2016-12-01

    The existence of an inner source of pickup ions close to the Sun was proposed in order to explain the unexpected discovery of C+ in the high-speed polar solar wind. Here I report on detailed analyses of the composition and the radial and latitudinal variations of inner source pickup ions measured with the Solar Wind Ion Composition Spectrometer on Ulysses from 1991 to 1998, approaching and during solar minimum. We find that the C+ intensity drops off with radial distance R as R-1.53, peaks at mid latitudes and drops to its lowest value in the ecliptic. Not only was C+ observed, but also N+, O+, Ne+, Na+, Mg+, Ar+, S+, K+, CH+, NH+, OH+, H2O+, H3O+, MgH+, HCN+, C2H4+, SO+ and many other singly-charged heavy ions and molecular ions. The measured velocity distributions of inner source pickup C+ and O+ indicate that these inner source pickup ions are most likely produced by charge exchange, photoionization and electron impact ionization of neutrals close to the Sun (within 10 to 30 solar radii). Possible causes for the unexpected latitudinal variations and the neutral source(s) producing the inner source pickup ions as well as plausible production mechanisms for inner source pickup ions will be discussed.

  18. Nanoplatform-based molecular imaging

    National Research Council Canada - National Science Library

    Chen, Xiaoyuan

    2011-01-01

    "Nanoplathform-Based Molecular Imaging provides rationale for using nanoparticle-based probes for molecular imaging, then discusses general strategies for this underutilized, yet promising, technology...

  19. Cardiovascular Molecular Imaging

    International Nuclear Information System (INIS)

    Lee, Kyung Han

    2009-01-01

    Molecular imaging strives to visualize processes in living subjects at the molecular level. Monitoring biochemical processes at this level will allow us to directly track biological processes and signaling events that lead to pathophysiological abnormalities, and help make personalized medicine a reality by allowing evaluation of therapeutic efficacies on an individual basis. Although most molecular imaging techniques emerged from the field of oncology, they have now gradually gained acceptance by the cardiovascular community. Hence, the availability of dedicated high-resolution small animal imaging systems and specific targeting imaging probes is now enhancing our understanding of cardiovascular diseases and expediting the development of newer therapies. Examples include imaging approaches to evaluate and track the progress of recent genetic and cellular therapies for treatment of myocardial ischemia. Other areas include in vivo monitoring of such key molecular processes as angiogenesis and apoptosis. Cardiovascular molecular imaging is already an important research tool in preclinical experiments. The challenge that lies ahead is to implement these techniques into the clinics so that they may help fulfill the promise of molecular therapies and personalized medicine, as well as to resolve disappointments and controversies surrounding the field

  20. Molecular toxicity of nanomaterials.

    Science.gov (United States)

    Chang, Xue-Ling; Yang, Sheng-Tao; Xing, Gengmei

    2014-10-01

    With the rapid developments in the fields of nanoscience and nanotechnlogy, more and more nanomaterials and their based consumer products have been used into our daily life. The safety concerns of nanomaterials have been well recognized by the scientific community and the public. Molecular mechanism of interactions between nanomaterials and biosystems is the most essential topic and final core of the biosafety. In the last two decades, nanotoxicology developed very fast and toxicity phenomena of nanomaterials have been reported. To achieve better understanding and detoxication of nanomaterials, thorough studies of nanotoxicity at molecular level are important. The interactions between nanomaterials and biomolecules have been widely investigated as the first step toward the molecular nanotoxicology. The consequences of such interactions have been discussed in the literature. Besides this, the chemical mechanism of nanotoxicology is gaining more attention, which would lead to a better design of nontoxic nanomaterials. In this review, we focus on the molecular nanotoxicology and explore the toxicity of nanomaterials at molecular level. The molecular level studies of nanotoxicology are summarized and the published nanotoxicological data are revisited.

  1. Environmental research at the Advanced Photon Source

    International Nuclear Information System (INIS)

    Kemner, K.M.; Boyanov, M.I.; Eng, P.; Fenter, P.; Heald, S.; Lai, B.; Lee, S.S.; Scheckel, K.G.; Skanthakumar, S.; Sutton, S.R.; Wilson, R.E.

    2010-01-01

    Because of the importance of probing molecular-scale chemical and physical structure of environmental samples in their natural and often hydrated state, synchrotron radiation has been a powerful tool for environmental scientists for decades. Thus, the crucial role that a highly coherent and high-brightness hard X-ray source such as the Advance Photon Source (APS) can play in addressing many of the outstanding questions in molecular environmental science (MES) was recognized even before 'first light' at the facility. No single synchrotron-based technique or experimental approach can adequately address the tremendous temporal and spatial heterogeneities of the chemistry, physics, and biology of natural environmental samples. Thus, it is common at the APS that multiple X-ray techniques and experimental systems are employed to investigate environmental samples, often chosen for their ability to focus on solute species, plants, microbes, organics, interfacial species, or solids.

  2. 2011 NATA - Emissions Sources

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset includes all emissions sources that were modeled in the 2011 National Air Toxics Assessment (NATA), inlcluding point, nonpoint, and mobile sources, and...

  3. Biogenic Emission Sources

    Science.gov (United States)

    Biogenic emissions sources come from natural sources and need to accounted for in photochemical grid models. They are computed using a model which utilizes spatial information on vegetation and land use.

  4. Spallation Neutron Source (SNS)

    Data.gov (United States)

    Federal Laboratory Consortium — The SNS at Oak Ridge National Laboratory is a next-generation spallation neutron source for neutron scattering that is currently the most powerful neutron source in...

  5. EPA's Radioactive Source Program

    International Nuclear Information System (INIS)

    Kopsick, D.

    2004-01-01

    The US EPA is the lead Federal agency for emergency responses to unknown radiological materials, not licensed, owned or operated by a Federal agency or an Agreement state (Federal Radiological Emergency Response Plan, 1996). The purpose of EPA's clean materials programme is to keep unwanted and unregulated radioactive material out of the public domain. This is achieved by finding and securing lost sources, maintaining control of existing sources and preventing future losses. The focus is on both, domestic and international fronts. The domestic program concentrates on securing lost sources, preventing future losses, alternative technologies like tagging of radioactive sources in commerce, pilot radioactive source roundup, training programs, scrap metal and metal processing facilities, the demolition industry, product stewardship and alternatives to radioactive devices (fewer radioactive source devices means fewer orphan sources). The international program consists of securing lost sources, preventing future losses, radiation monitoring of scrap metal at ports and the international scrap metal monitoring protocol

  6. Dioxin emissions and sources

    International Nuclear Information System (INIS)

    1994-01-01

    The papers presented at the seminar discussed dioxin emissions and sources, dioxin pollution of soils, waste water and sewage sludge, stocktaking of emission sources, and exposure and risk analyses for dioxin and other pollutants. (EF) [de

  7. Sealed radioactive source management

    International Nuclear Information System (INIS)

    2005-01-01

    Sealed radioactive sources have been used in a wide range of application in medicine, agriculture, geology, industry and other fields. Since its utilization many sources have become out of use and became waste but no proper management. This has lead to many accidents causing deaths and serious radiation injuries worldwide. Spent sources application is expanding but their management has seen little improvements. Sealed radioactive sources have become a security risk calling for prompt action. Source management helps to maintain sources in a good physical status and provide means of source tracking and control. It also provides a well documented process of the sources making any future management options safe, secure and cost effective. Last but not least good source management substantially reduces the risk of accidents and eliminates the risk of malicious use. The International Atomic Energy Agency assists Member States to build the infrastructure to properly manage sealed radioactive sources. The assistance includes training of national experts to handle, condition and properly store the sources. For Member States that do not have proper facilities, we provide the technical assistance to design a proper facility to properly manage the radioactive sources and provide for their proper storage. For Member States that need to condition their sources properly but don't have the required infrastructure we provide direct assistance to physically help them with source recovery and provide an international expert team to properly condition their sources and render them safe and secure. We offer software (Radioactive Waste Management Registry) to properly keep a complete record on the sources and provide for efficient tracking. This also helps with proper planning and decision making for long term management

  8. Digital intelligence sources transporter

    International Nuclear Information System (INIS)

    Zhang Zhen; Wang Renbo

    2011-01-01

    It presents from the collection of particle-ray counting, infrared data communication, real-time monitoring and alarming, GPRS and other issues start to realize the digital management of radioactive sources, complete the real-time monitoring of all aspects, include the storing of radioactive sources, transporting and using, framing intelligent radioactive sources transporter, as a result, achieving reliable security supervision of radioactive sources. (authors)

  9. Nanotechnology Review: Molecular Electronics to Molecular Motors

    Science.gov (United States)

    Srivastava, Deepak; Saini, Subhash (Technical Monitor)

    1998-01-01

    Reviewing the status of current approaches and future projections, as already published in scientific journals and books, the talk will summarize the direction in which computational and experimental nanotechnologies are progressing. Examples of nanotechnological approaches to the concepts of design and simulation of carbon nanotube based molecular electronic and mechanical devices will be presented. The concepts of nanotube based gears and motors will be discussed. The above is a non-technical review talk which covers long term precompetitive basic research in already published material that has been presented before many US scientific meeting audiences.

  10. Spallation neutron sources

    International Nuclear Information System (INIS)

    Fraser, J.S.; Bartholomew, G.A.

    1983-01-01

    The principles and theory of spallation neutron sources are outlined and a comparison is given with other types of neutron source. A summary of the available accelerator types for spallation neutron sources and their advantages and disadvantages is presented. Suitable target materials are discussed for specific applications, and typical target assemblies shown. (U.K.)

  11. Global Sourcing of Services

    DEFF Research Database (Denmark)

    Ørberg Jensen, Peter D.; Petersen, Bent

    2013-01-01

    The global sourcing of services offers high returns but is also associated with high risks. The extent to which firms engage in ‘transformational’ global sourcing (i.e., global sourcing implying considerable changes in the home organization) chiefly depends on management's comfort zone which...

  12. Sources of pulsed radiation

    International Nuclear Information System (INIS)

    Sauer, M.C. Jr.

    1981-01-01

    Characteristics of various sources of pulsed radiation are examined from the viewpoint of their importance to the radiation chemist, and some examples of uses of such sources are mentioned. A summary is given of the application of methods of physical dosimetry to pulsed sources, and the calibration of convenient chemical dosimeters by physical dosimetry is outlined. 7 figures, 1 table

  13. Investigating Primary Source Literacy

    Science.gov (United States)

    Archer, Joanne; Hanlon, Ann M.; Levine, Jennie A.

    2009-01-01

    Primary source research requires students to acquire specialized research skills. This paper presents results from a user study testing the effectiveness of a Web guide designed to convey the concepts behind "primary source literacy". The study also evaluated students' strengths and weaknesses when conducting primary source research. (Contains 3…

  14. Open Source Business Solutions

    Directory of Open Access Journals (Sweden)

    Ion IVAN

    2008-01-01

    Full Text Available This analyses the Open source movement. Open source development process and management is seen different from the classical point of view. This focuses on characteristics and software market tendencies for the main Open source initiatives. It also points out the labor market future evolution for the software developers.

  15. Argonne inverted sputter source

    International Nuclear Information System (INIS)

    Yntema, J.L.; Billquist, P.J.

    1983-01-01

    The emittance of the inverted sputter source with immersion lenses was measured to be about 5π mm mrad MeV/sup 1/2/ at the 75% level over a wide range of beam intensities. The use of the source in experiments with radioactive sputter targets and hydrogen loaded targets is described. Self contamination of the source is discussed

  16. Improved Ambient Pressure Pyroelectric Ion Source

    Science.gov (United States)

    Beegle, Luther W.; Kim, Hugh I.; Kanik, Isik; Ryu, Ernest K.; Beckett, Brett

    2011-01-01

    The detection of volatile vapors of unknown species in a complex field environment is required in many different applications. Mass spectroscopic techniques require subsystems including an ionization unit and sample transport mechanism. All of these subsystems must have low mass, small volume, low power, and be rugged. A volatile molecular detector, an ambient pressure pyroelectric ion source (APPIS) that met these requirements, was recently reported by Caltech researchers to be used in in situ environments.

  17. Development of an electrically driven molecular motor.

    Science.gov (United States)

    Murphy, Colin J; Sykes, E Charles H

    2014-10-01

    For molecules to be used as components in molecular machinery, methods are required that couple individual molecules to external energy sources in order to selectively excite motion in a given direction. While significant progress has been made in the construction of synthetic molecular motors powered by light and by chemical reactions, there are few experimental examples of electrically driven molecular motors. To this end, we pioneered the use of a new, stable and tunable molecular rotor system based on surface-bound thioethers to comprehensively study many aspects of molecular rotation. As biological molecular motors often operate at interfaces, our synthetic system is especially amenable to microscopic interrogation as compared to solution-based systems. Using scanning tunneling microscopy (STM) and density functional theory, we studied the rotation of surface-bound thioethers, which can be induced either thermally or by electrons from the STM tip in a two-terminal setup. Moreover, the temperature and electron flux can be adjusted to allow each rotational event to be monitored at the molecular scale in real time. This work culminated in the first experimental demonstration of a single-molecule electric motor, where the electrically driven rotation of a butyl methyl sulfide molecule adsorbed on a copper surface could be directionally biased. The direction and rate of the rotation are related to the chirality of both the molecule and the STM tip (which serves as the electrode), illustrating the importance of the symmetry of the metal contacts in atomic-scale electrical devices. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Source splitting via the point source method

    International Nuclear Information System (INIS)

    Potthast, Roland; Fazi, Filippo M; Nelson, Philip A

    2010-01-01

    We introduce a new algorithm for source identification and field splitting based on the point source method (Potthast 1998 A point-source method for inverse acoustic and electromagnetic obstacle scattering problems IMA J. Appl. Math. 61 119–40, Potthast R 1996 A fast new method to solve inverse scattering problems Inverse Problems 12 731–42). The task is to separate the sound fields u j , j = 1, ..., n of n element of N sound sources supported in different bounded domains G 1 , ..., G n in R 3 from measurements of the field on some microphone array—mathematically speaking from the knowledge of the sum of the fields u = u 1 + ... + u n on some open subset Λ of a plane. The main idea of the scheme is to calculate filter functions g 1 ,…, g n , n element of N, to construct u l for l = 1, ..., n from u| Λ in the form u l (x) = ∫ Λ g l,x (y)u(y)ds(y), l=1,... n. (1) We will provide the complete mathematical theory for the field splitting via the point source method. In particular, we describe uniqueness, solvability of the problem and convergence and stability of the algorithm. In the second part we describe the practical realization of the splitting for real data measurements carried out at the Institute for Sound and Vibration Research at Southampton, UK. A practical demonstration of the original recording and the splitting results for real data is available online

  19. Thermal neutron source study

    International Nuclear Information System (INIS)

    Holden, T.M.

    1983-05-01

    The value of intense neutron beams for condensed matter research is discussed with emphasis on the complementary nature of steady state and pulsed neutron sources. A large body of information on neutron sources, both existing and planned, is then summarized under four major headings: fission reactors, electron accelerators with heavy metal targets, pulsed spallation sources and 'steady state' spallation sources. Although the cost of a spallation source is expected to exceed that of a fission reactor of the same flux by a factor of two, there are significant advantages for a spallation device such as the proposed Electronuclear Materials Test Facility (EMTF)

  20. Spallation neutrons pulsed sources

    International Nuclear Information System (INIS)

    Carpenter, J.

    1996-01-01

    This article describes the range of scientific applications which can use these pulsed neutrons sources: Studies on super fluids, measures to verify the crawling model for the polymers diffusion; these sources are also useful to study the neutron disintegration, the ultra cold neutrons. In certain applications which were not accessible by neutrons diffusion, for example, radiations damages, radionuclides production and activation analysis, the spallation sources find their use and their improvement will bring new possibilities. Among others contributions, one must notice the place at disposal of pulsed muons sources and neutrinos sources. (N.C.). 3 figs

  1. Compact microwave ion source

    International Nuclear Information System (INIS)

    Leung, K.N.; Walther, S.; Owren, H.W.

    1985-05-01

    A small microwave ion source has been fabricated from a quartz tube with one end enclosed by a two grid accelerator. The source is also enclosed by a cavity operated at a frequency of 2.45 GHz. Microwave power as high as 500 W can be coupled to the source plasma. The source has been operated with and without multicusp fields for different gases. In the case of hydrogen, ion current density of 200 mA/cm -2 with atomic ion species concentration as high as 80% has been extracted from the source

  2. Sources for charged particles

    International Nuclear Information System (INIS)

    Arianer, J.

    1997-01-01

    This document is a basic course on charged particle sources for post-graduate students and thematic schools on large facilities and accelerator physics. A simple but precise description of the creation and the emission of charged particles is presented. This course relies on every year upgraded reference documents. Following relevant topics are considered: electronic emission processes, technological and practical considerations on electron guns, positron sources, production of neutral atoms, ionization, plasma and discharge, different types of positive and negative ion sources, polarized particle sources, materials for the construction of ion sources, low energy beam production and transport. (N.T.)

  3. Polarized source upgrading

    International Nuclear Information System (INIS)

    Clegg, T.B.; Rummel, R.L.; Carter, E.P.; Westerfeldt, C.R.; Lovette, A.W.; Edwards, S.E.

    1985-01-01

    The decision was made this past year to move the Lamb-shift polarized ion source which was first installed in the laboratory in 1970. The motivation was the need to improve the flexibility of spin-axis orientation by installing the ion source with a new Wien-filter spin precessor which is capable of rotating physically about the beam axis. The move of the polarized source was accomplished in approximately two months, with the accelerator being turned off for experiments during approximately four weeks of this time. The occasion of the move provided the opportunity to rewire completely the entire polarized ion source frame and to rebuild approximately half of the electronic chassis on the source. The result is an ion source which is now logically wired and carefully documented. Beams obtained from the source are much more stable than those previously available

  4. Polarized electron sources

    International Nuclear Information System (INIS)

    Clendenin, J.E.

    1995-05-01

    Polarized electron sources for high energy accelerators took a significant step forward with the introduction of a new laser-driven photocathode source for the SLC in 1992. With an electron beam polarization of >80% and with ∼99% uptime during continuous operation, this source is a key factor in the success of the current SLC high-energy physics program. The SLC source performance is used to illustrate both the capabilities and the limitations of solid-state sources. The beam requirements for future colliders are similar to that of the SLC with the addition in most cases of multiple-bunch operation. A design for the next generation accelerator source that can improve the operational characteristics and at least minimize some of the inherent limitations of present sources is presented. Finally, the possibilities for producing highly polarized electron beams for high-duty-factor accelerators are discussed

  5. Wavelength sweepable laser source

    DEFF Research Database (Denmark)

    2014-01-01

    Wavelength sweepable laser source is disclosed, wherein the laser source is a semiconductor laser source adapted for generating laser light at a lasing wavelength. The laser source comprises a substrate, a first reflector, and a second reflector. The first and second reflector together defines...... and having a rest position, the second reflector and suspension together defining a microelectromechanical MEMS oscillator. The MEMS oscillator has a resonance frequency and is adapted for oscillating the second reflector on either side of the rest position.; The laser source further comprises electrical...... connections adapted for applying an electric field to the MEMS oscillator. Furthermore, a laser source system and a method of use of the laser source are disclosed....

  6. Molecular dewetting on insulators

    International Nuclear Information System (INIS)

    Burke, S A; Topple, J M; Gruetter, P

    2009-01-01

    Recent attention given to the growth and morphology of organic thin films with regard to organic electronics has led to the observation of dewetting (a transition from layer(s) to islands) of molecular deposits in many of these systems. Dewetting is a much studied phenomenon in the formation of polymer and liquid films, but its observation in thin films of the 'small' molecules typical of organic electronics requires additional consideration of the structure of the interface between the molecular film and the substrate. This review covers some key concepts related to dewetting and molecular film growth. In particular, the origins of different growth modes and the thickness dependent interactions which give rise to dewetting are discussed in terms of surface energies and the disjoining pressure. Characteristics of molecular systems which may lead to these conditions, including the formation of metastable interface structures and commensurate-incommensurate phase transitions, are also discussed. Brief descriptions of some experimental techniques which have been used to study molecular dewetting are given as well. Examples of molecule-on-insulator systems which undergo dewetting are described in some detail, specifically perylene derivatives on alkali halides, C 60 on alkali halides, and the technologically important system of pentacene on SiO 2 . These examples point to some possible predicting factors for the occurrence of dewetting, most importantly the formation of an interface layer which differs from the bulk crystal structure. (topical review)

  7. Molecular dewetting on insulators.

    Science.gov (United States)

    Burke, S A; Topple, J M; Grütter, P

    2009-10-21

    Recent attention given to the growth and morphology of organic thin films with regard to organic electronics has led to the observation of dewetting (a transition from layer(s) to islands) of molecular deposits in many of these systems. Dewetting is a much studied phenomenon in the formation of polymer and liquid films, but its observation in thin films of the 'small' molecules typical of organic electronics requires additional consideration of the structure of the interface between the molecular film and the substrate. This review covers some key concepts related to dewetting and molecular film growth. In particular, the origins of different growth modes and the thickness dependent interactions which give rise to dewetting are discussed in terms of surface energies and the disjoining pressure. Characteristics of molecular systems which may lead to these conditions, including the formation of metastable interface structures and commensurate-incommensurate phase transitions, are also discussed. Brief descriptions of some experimental techniques which have been used to study molecular dewetting are given as well. Examples of molecule-on-insulator systems which undergo dewetting are described in some detail, specifically perylene derivatives on alkali halides, C(60) on alkali halides, and the technologically important system of pentacene on SiO(2). These examples point to some possible predicting factors for the occurrence of dewetting, most importantly the formation of an interface layer which differs from the bulk crystal structure.

  8. Phylogenetic molecular function annotation

    International Nuclear Information System (INIS)

    Engelhardt, Barbara E; Jordan, Michael I; Repo, Susanna T; Brenner, Steven E

    2009-01-01

    It is now easier to discover thousands of protein sequences in a new microbial genome than it is to biochemically characterize the specific activity of a single protein of unknown function. The molecular functions of protein sequences have typically been predicted using homology-based computational methods, which rely on the principle that homologous proteins share a similar function. However, some protein families include groups of proteins with different molecular functions. A phylogenetic approach for predicting molecular function (sometimes called 'phylogenomics') is an effective means to predict protein molecular function. These methods incorporate functional evidence from all members of a family that have functional characterizations using the evolutionary history of the protein family to make robust predictions for the uncharacterized proteins. However, they are often difficult to apply on a genome-wide scale because of the time-consuming step of reconstructing the phylogenies of each protein to be annotated. Our automated approach for function annotation using phylogeny, the SIFTER (Statistical Inference of Function Through Evolutionary Relationships) methodology, uses a statistical graphical model to compute the probabilities of molecular functions for unannotated proteins. Our benchmark tests showed that SIFTER provides accurate functional predictions on various protein families, outperforming other available methods.

  9. Molecular MR imaging

    International Nuclear Information System (INIS)

    Fleige, G.; Hamm, B.

    2000-01-01

    Basic medicobiological research in recent years has made rapid advances in the functional understanding of normal and pathological processes down to the molecular level. At the same time, various imaging modalities have developed from the depiction of organs to approaching the depiction of the cellular level and are about to make the visualization of molecular processes an established procedure. Besides other modalities like PET and near-infrared fluorescence, MR imaging offers some promising options for molecular imaging as well as some applications that have already been tested such as the visualization of enzyme activity, the depiction of the expression of certain genes, the visualization of surface receptors, or the specific demonstration of cells involved in the body's immune response. A major advantage of molecular magnetic resonance imaging (mMRI) over other more sensitive modalities is its high spatial resolution. However, the establishment of mMRI crucially relies on further improvements in resolution and the development of molecular markers for improving its sensitivity and specificity. The state of the art of mMRI is presented by giving a survey of the literature on experimental studies and reporting the results our study group obtained during investigation on gliomas. (orig.) [de

  10. Molecularly targeted therapeutic radiopharmaceuticals

    International Nuclear Information System (INIS)

    Saw, M.M.

    2007-01-01

    Full text: It is generally agreed that current focus of nuclear medicine development should be on molecular imaging and therapy. Though, the widespread use of the terminology 'molecular imaging' is quite recent, nuclear medicine has used molecular imaging techniques for more than 20 years ago. A variety of radiopharmaceuticals have been introduced for the internal therapy of malignant and inflammatory lesions in nuclear medicine. In the field of bio/medical imaging, nuclear medicine is one of the disciplines which has the privilege of organized and well developed chemistry/ pharmacy section; radio-chemistry/radiopharmacy. Fundamental principles have been developed more than 40 years ago and advanced research is going well into postgenomic era. The genomic revolution and dramatically increased insight in the molecular mechanisms underlying pathology have led to paradigm shift in drug development. Likewise does in the nuclear medicine. Here, the author will present current clinical and pre-clinical therapeutic radiopharmaceuticals based on molecular targets such as membrane-bound receptors, enzymes, nucleic acids, sodium iodide symporter, etc, in correlation with fundamentals of radiopharmacy. (author)

  11. Photon acceleration-based radiation sources

    International Nuclear Information System (INIS)

    Hoffman, J. R.; Muggli, P.; Katsouleas, T.; Mori, W. B.; Joshi, C.

    1999-01-01

    The acceleration and deceleration of photons in a plasma provides the means for a series of new radiation sources. Previous work on a DC to AC Radiation Converter (DARC source) has shown variable acceleration of photons having zero frequency (i.e., an electrostatic field) to between 6 and 100 GHz (1-3). These sources all had poor guiding characteristics resulting in poor power coupling from the source to the load. Continuing research has identified a novel way to integrate the DARC source into a waveguide. The so called ''pin structure'' uses stainless steel pins inserted through the narrow side of an X band waveguide to form the electrostatic field pattern (k≠0, ω=0). The pins are spaced such that the absorption band resulting from this additional periodic structure is outside of the X band range (8-12 GHz), in which the normal waveguide characteristics are left unchanged. The power of this X band source is predicted theoretically to scale quadratically with the pin bias voltage as -800 W/(kV) 2 and have a pulse width of -1 ns. Cold tests and experimental results are presented. Applications for a high power, short pulse radiation source extends to the areas of landmine detection, improved radar resolution, and experimental investigations of molecular systems

  12. Testing the molecular clock using mechanistic models of fossil preservation and molecular evolution.

    Science.gov (United States)

    Warnock, Rachel C M; Yang, Ziheng; Donoghue, Philip C J

    2017-06-28

    Molecular sequence data provide information about relative times only, and fossil-based age constraints are the ultimate source of information about absolute times in molecular clock dating analyses. Thus, fossil calibrations are critical to molecular clock dating, but competing methods are difficult to evaluate empirically because the true evolutionary time scale is never known. Here, we combine mechanistic models of fossil preservation and sequence evolution in simulations to evaluate different approaches to constructing fossil calibrations and their impact on Bayesian molecular clock dating, and the relative impact of fossil versus molecular sampling. We show that divergence time estimation is impacted by the model of fossil preservation, sampling intensity and tree shape. The addition of sequence data may improve molecular clock estimates, but accuracy and precision is dominated by the quality of the fossil calibrations. Posterior means and medians are poor representatives of true divergence times; posterior intervals provide a much more accurate estimate of divergence times, though they may be wide and often do not have high coverage probability. Our results highlight the importance of increased fossil sampling and improved statistical approaches to generating calibrations, which should incorporate the non-uniform nature of ecological and temporal fossil species distributions. © 2017 The Authors.

  13. Uncertainty estimates for theoretical atomic and molecular data

    International Nuclear Information System (INIS)

    Chung, H-K; Braams, B J; Bartschat, K; Császár, A G; Drake, G W F; Kirchner, T; Kokoouline, V; Tennyson, J

    2016-01-01

    Sources of uncertainty are reviewed for calculated atomic and molecular data that are important for plasma modeling: atomic and molecular structures and cross sections for electron-atom, electron-molecule, and heavy particle collisions. We concentrate on model uncertainties due to approximations to the fundamental many-body quantum mechanical equations and we aim to provide guidelines to estimate uncertainties as a routine part of computations of data for structure and scattering. (topical review)

  14. Evolutionary molecular medicine.

    Science.gov (United States)

    Nesse, Randolph M; Ganten, Detlev; Gregory, T Ryan; Omenn, Gilbert S

    2012-05-01

    Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

  15. [Molecular techniques in mycology].

    Science.gov (United States)

    Rodríguez-Tudela, Juan Luis; Cuesta, Isabel; Gómez-López, Alicia; Alastruey-Izquierdo, Ana; Bernal-Martínez, Leticia; Cuenca-Estrella, Manuel

    2008-11-01

    An increasing number of molecular techniques for the diagnosis of fungal infections have been developed in the last few years, due to the growing prevalence of mycoses and the length of time required for diagnosis when classical microbiological methods are used. These methods are designed to resolve the following aspects of mycological diagnosis: a) Identification of fungi to species level by means of sequencing relevant taxonomic targets; b) early clinical diagnosis of invasive fungal infections; c) detection of molecular mechanisms of resistance to antifungal agents; and d) molecular typing of fungi. Currently, these methods are restricted to highly developed laboratories. However, some of these techniques will probably be available in daily clinical practice in the near future.

  16. Theoretical Molecular Biophysics

    CERN Document Server

    Scherer, Philipp

    2010-01-01

    "Theoretical Molecular Biophysics" is an advanced study book for students, shortly before or after completing undergraduate studies, in physics, chemistry or biology. It provides the tools for an understanding of elementary processes in biology, such as photosynthesis on a molecular level. A basic knowledge in mechanics, electrostatics, quantum theory and statistical physics is desirable. The reader will be exposed to basic concepts in modern biophysics such as entropic forces, phase separation, potentials of mean force, proton and electron transfer, heterogeneous reactions coherent and incoherent energy transfer as well as molecular motors. Basic concepts such as phase transitions of biopolymers, electrostatics, protonation equilibria, ion transport, radiationless transitions as well as energy- and electron transfer are discussed within the frame of simple models.

  17. Molecular Diagnosis of Tuberculosis.

    Science.gov (United States)

    Nurwidya, Fariz; Handayani, Diah; Burhan, Erlina; Yunus, Faisal

    2018-01-01

    Tuberculosis (TB) is one of the leading causes of adult death in the Asia-Pacific Region, including Indonesia. As an infectious disease caused by Mycobacterium tuberculosis (MTB), TB remains a major public health issue especially in developing nations due to the lack of adequate diagnostic testing facilities. Diagnosis of TB has entered an era of molecular detection that provides faster and more cost-effective methods to diagnose and confirm drug resistance in TB cases, meanwhile, diagnosis by conventional culture systems requires several weeks. New advances in the molecular detection of TB, including the faster and simpler nucleic acid amplification test (NAAT) and whole-genome sequencing (WGS), have resulted in a shorter time for diagnosis and, therefore, faster TB treatments. In this review, we explored the current findings on molecular diagnosis of TB and drug-resistant TB to see how this advancement could be integrated into public health systems in order to control TB.

  18. Orphan sources in Slovenia

    International Nuclear Information System (INIS)

    Janzekovic, H.; Cesarek, J.

    2005-01-01

    For decades the international standards and requirements postulate severe control over all lifecycle phases of radioactive sources in order to prevent risks associated with exposure of people and the environment. Despite this fact the orphan sources became a serious problem as a consequence of enlargement of economic transactions in many countries in Europe as well as in the world. The countries as well as international organisations, aware of this emerging problem, are trying to gain control over orphan sources using different approaches. These approaches include control over sources before they could become orphan sources. In addition, countries are also developing action plans in case that an orphan source could be found. The problems related to orphan sources in Slovenia is discussed based on the case studies from the last years. While in the nineties of the last century just a few cases of orphan sources were identified their number has increased substantially since 2003. The paper discusses the general reasons for the phenomena of orphan sources as well as the experience related to regaining control over orphan sources. (author)

  19. Infrared reflection nebulae in Orion Molecular Cloud

    International Nuclear Information System (INIS)

    Pendleton, Y.; Werner, M.W.; Capps, R.; Lester, D.; Hawaii Univ., Honolulu; Texas Univ., Austin)

    1986-01-01

    New observations of Orion Molecular Cloud 2 have been made from 1 to 100 microns using the NASA Infrared Telescope Facility and the Kuiper Airborne Observatory. An extensive program of polarimetry, photometry, and spectrophotometry has shown that the extended emission regions associated with two of the previously known near-infrared sources, IRS 1 and IRS 4, are infrared reflection nebulae, and that the compact sources IRS 1 and IRS 4 are the main luminosity sources in the cloud. The constraints from the far-infrared observations and an analysis of the scattered light from the IRS 1 nebula show that OMC-2/IRS 1 can be characterized by L of 500 solar luminosities or less and T of roughly 1000 K. The near-infrared albedo of the grains in the IRS 1 nebula is greater than 0.08. 27 references

  20. Synergetics of molecular systems

    CERN Document Server

    Lupichev, Lev N; Kadantsev, Vasiliy N

    2014-01-01

    Synergetics is the quantitative study of multicomponent systems that exhibit nonlinear dynamics and cooperativity. This book specifically considers basic models of the nonlinear dynamics of molecular systems and discusses relevant applications in biological physics and the polymer sciences.Emphasis is placed on specific solutions to the dynamical equations that correspond to the coherent formation of spatial-temporal structures, such as solitons, kinks and breathers, in particular. The emergence of these patterns in molecular structures provides a variety of information on their structural pro

  1. Molecular environmental geochemistry

    Science.gov (United States)

    O'Day, Peggy A.

    1999-05-01

    The chemistry, mobility, and bioavailability of contaminant species in the natural environment are controlled by reactions that occur in and among solid, aqueous, and gas phases. These reactions are varied and complex, involving changes in chemical form and mass transfer among inorganic, organic, and biochemical species. The field of molecular environmental geochemistry seeks to apply spectroscopic and microscopic probes to the mechanistic understanding of environmentally relevant chemical processes, particularly those involving contaminants and Earth materials. In general, empirical geochemical models have been shown to lack uniqueness and adequate predictive capability, even in relatively simple systems. Molecular geochemical tools, when coupled with macroscopic measurements, can provide the level of chemical detail required for the credible extrapolation of contaminant reactivity and bioavailability over ranges of temperature, pressure, and composition. This review focuses on recent advances in the understanding of molecular chemistry and reaction mechanisms at mineral surfaces and mineral-fluid interfaces spurred by the application of new spectroscopies and microscopies. These methods, such as synchrotron X-ray absorption and scattering techniques, vibrational and resonance spectroscopies, and scanning probe microscopies, provide direct chemical information that can elucidate molecular mechanisms, including element speciation, ligand coordination and oxidation state, structural arrangement and crystallinity on different scales, and physical morphology and topography of surfaces. Nonvacuum techniques that allow examination of reactions in situ (i.e., with water or fluids present) and in real time provide direct links between molecular structure and reactivity and measurements of kinetic rates or thermodynamic properties. Applications of these diverse probes to laboratory model systems have provided fundamental insight into inorganic and organic reactions at

  2. Molecular cardiovascular imaging

    International Nuclear Information System (INIS)

    Schaefers, M.

    2007-01-01

    Although huge and long-lasting research efforts have been spent on the development of new diagnostic techniques investigating cardiovascular diseases, still fundamental challenges exist; the main challenge being the diagnosis of a suspected or known coronary artery disease or its consequences (myocardial infarction, heart failure etc.). Beside morphological techniques, functional imaging modalities are available in clinical diagnostic algorithms, whereas molecular cardiovascular imaging techniques are still under development. This review summarizes clinical-diagnostical challenges of modern cardiovascular medicine as well as the potential of new molecular imaging techniques to face these. (orig.)

  3. Targeted molecular imaging

    International Nuclear Information System (INIS)

    Kim, E. Edmund

    2003-01-01

    Molecular imaging aims to visualize the cellular and molecular processes occurring in living tissues, and for the imaging of specific molecules in vivo, the development of reporter probes and dedicated imaging equipment is most important. Reporter genes can be used to monitor the delivery and magnitude of therapeutic gene transfer, and the time variation involved. Imaging technologies such as micro-PET, SPECT, MRI and CT, as well as optical imaging systems, are able to non-invasively detect, measure, and report the simultaneous expression of multiple meaningful genes. It is believed that recent advances in reporter probes, imaging technologies and gene transfer strategies will enhance the effectiveness of gene therapy trials

  4. Molecular epidemiology of Blastocystis

    Directory of Open Access Journals (Sweden)

    Fadime Eroğlu

    2015-12-01

    Full Text Available Blastocystis pathogenicity and classification was newly illuminated with molecular genetic studies and recently the parasite was found in the focus of many researchers. Several molecular methods such as; polymerase chain reaction (PCR, PCR-restriction fragment length polymorphism, random amplified polymorphic DNA, real-time polymerase chain reaction and DNA sequencing analyses can be used in genotyping of Blastocystis. Blastocystis parasites may cause diarrhea, abdominal pain, bloating, gas, irritability, anorexia, cramps, vomiting, dehydration, insomnia, nausea, loss of appetite, weight loss, fatigue symptoms and also could be asymptomatic cases. In this review, it was aimed to summarize the associations between Blastocystis subtypes and pathogenicity.

  5. Valency and molecular structure

    CERN Document Server

    Cartmell, E

    1977-01-01

    Valency and Molecular Structure, Fourth Edition provides a comprehensive historical background and experimental foundations of theories and methods relating to valency and molecular structures. In this edition, the chapter on Bohr theory has been removed while some sections, such as structures of crystalline solids, have been expanded. Details of structures have also been revised and extended using the best available values for bond lengths and bond angles. Recent developments are mostly noted in the chapter on complex compounds, while a new chapter has been added to serve as an introduction t

  6. Ionic and Molecular Liquids

    DEFF Research Database (Denmark)

    Chaban, Vitaly V.; Prezhdo, Oleg

    2013-01-01

    Because of their outstanding versatility, room-temperature ionic liquids (RTILs) are utilized in an ever increasing number of novel and fascinating applications, making them the Holy Grail of modern materials science. In this Perspective, we address the fundamental research and prospective...... applications of RTILs in combination with molecular liquids, concentrating on three significant areas: (1) the use of molecular liquids to decrease the viscosity of RTILs; (2) the role of RTIL micelle formation in water and organic solvents; and (3) the ability of RTILs to adsorb pollutant gases. Current...

  7. Molecular confocal laser endomicroscopy

    DEFF Research Database (Denmark)

    Karstensen, John Gásdal; Klausen, Pia Helene; Saftoiu, Adrian

    2014-01-01

    While flexible endoscopy is essential for macroscopic evaluation, confocal laser endomicroscopy (CLE) has recently emerged as an endoscopic method enabling visualization at a cellular level. Two systems are currently available, one based on miniprobes that can be inserted via a conventional...... during on-going endoscopy), a novel world of molecular evaluation opens up. The method of molecular CLE could potentially be used for estimating the expression of important receptors in carcinomas, subsequently resulting in immediate individualization of treatment regimens, but also for improving...

  8. Shocked molecular hydrogen in the supernova remnant IC 443

    International Nuclear Information System (INIS)

    Burton, M.G.; Brand, P.W.J.L.; Webster, A.S.

    1988-01-01

    Emission from the υ = 1-0 S(1) line of molecular hydrogen has been mapped over a section of the supernova remnant IC 443. The emission originates in a sinuous ridge where the expanding shell of the SNR is interacting with a molecular cloud. The relative intensities of the 1-0 S(1), 1-0 S(0) and 2-1 S(1) lines at 2.1-2.2 μm were measured and found to be characteristic of shock-excitation of the gas. The ridge shows bright spots which are possibly density enhancements in the molecular cloud. The total luminosity of the molecular hydrogen lines in the mapped region is estimated to be about 1000 times the solar luminosity, making IC 443 one of the most luminous galactic molecular hydrogen sources yet detected. (author)

  9. The future of nanofabrication and molecular scale devices in nanomedicine.

    Science.gov (United States)

    Freitas, R A

    2002-01-01

    Nanotechnology is engineering and manufacturing at the molecular scale, and the application of nanotechnology to medicine is called nanomedicine. Nanomedicine subsumes three mutually overlapping and progressively more powerful molecular technologies. First, nanoscale-structured materials and devices that can be fabricated today hold great promise for advanced diagnostics and biosensors, targeted drug delivery and smart drugs, and immunoisolation therapies. Second, biotechnology offers the benefits of molecular medicine via genomics, proteomics, and artificial engineered microbes. Third, in the longer term, molecular machine systems and medical nanorobots will allow instant pathogen diagnosis and extermination, chromosome replacement and individual cell surgery in vivo, and the efficient augmentation and improvement of natural physiological function. Current research is exploring the fabrication of designed nanostructures, nanoactuators and nanomotors, microscopic energy sources, and nanocomputers at the molecular scale, along with the means to assemble them into larger systems, economically and in great numbers.

  10. Point Pollution Sources Dimensioning

    Directory of Open Access Journals (Sweden)

    Georgeta CUCULEANU

    2011-06-01

    Full Text Available In this paper a method for determining the main physical characteristics of the point pollution sources is presented. It can be used to find the main physical characteristics of them. The main physical characteristics of these sources are top inside source diameter and physical height. The top inside source diameter is calculated from gas flow-rate. For reckoning the physical height of the source one takes into account the relation given by the proportionality factor, defined as ratio between the plume rise and physical height of the source. The plume rise depends on the gas exit velocity and gas temperature. That relation is necessary for diminishing the environmental pollution when the production capacity of the plant varies, in comparison with the nominal one.

  11. Specification of brachytherapy sources

    Energy Technology Data Exchange (ETDEWEB)

    1984-10-01

    BCRU recommends that the following specification of gamma-ray brachytherapy sources be adopted. Unless otherwise stated, the output of a cylindrical source should be specified in air kerma rate at a point in free space at a distance of 1 m from the source on the radial plane of symmetry, i.e. the plane bisecting the active length and perpendicular to the cylindrical axis of the source. For a wire source the output should be specified for a 1 cm length. For any other construction of source, the point at which the output is specified should be stated. It is also recommended that the units in which the air kerma rate is expressed should be micrograys per hour (..mu..Gy/h).

  12. Global Sourcing Flexibility

    DEFF Research Database (Denmark)

    Ørberg Jensen, Peter D.; Petersen, Bent

    2013-01-01

    the higher costs (but decreased risk for value chain disruption) embedded in a more flexible global sourcing model that allows the firm to replicate and/or relocate activities across multiple locations. We develop a model and propositions on facilitating and constraining conditions of global sourcing...... sourcing flexibility. Here we draw on prior research in the fields of organizational flexibility, international business and global sourcing as well as case examples and secondary studies. In the second part of the paper, we discuss the implications of global sourcing flexibility for firm strategy...... and operations against the backdrop of the theory-based definition of the construct. We discuss in particular the importance of global sourcing flexibility for operational performance stability, and the trade-off between specialization benefits, emerging from location and service provider specialization, versus...

  13. On simulation of local fluxes in molecular junctions

    Science.gov (United States)

    Cabra, Gabriel; Jensen, Anders; Galperin, Michael

    2018-05-01

    We present a pedagogical review of the current density simulation in molecular junction models indicating its advantages and deficiencies in analysis of local junction transport characteristics. In particular, we argue that current density is a universal tool which provides more information than traditionally simulated bond currents, especially when discussing inelastic processes. However, current density simulations are sensitive to the choice of basis and electronic structure method. We note that while discussing the local current conservation in junctions, one has to account for the source term caused by the open character of the system and intra-molecular interactions. Our considerations are illustrated with numerical simulations of a benzenedithiol molecular junction.

  14. Rf power sources

    International Nuclear Information System (INIS)

    Allen, M.A.

    1988-05-01

    This paper covers RF power sources for accelerator applications. The approach has been with particular customers in mind. These customers are high energy physicists who use accelerators as experimental tools in the study of the nucleus of the atom, and synchrotron light sources derived from electron or positron storage rings. This paper is confined to electron-positron linear accelerators since the RF sources have always defined what is possible to achieve with these accelerators. 11 refs., 13 figs

  15. Pulsed spallation Neutron Sources

    International Nuclear Information System (INIS)

    Carpenter, J.M.

    1994-01-01

    This paper reviews the early history of pulsed spallation neutron source development at Argonne and provides an overview of existing sources world wide. A number of proposals for machines more powerful than currently exist are under development, which are briefly described. The author reviews the status of the Intense Pulsed Neutron Source, its instrumentation, and its user program, and provides a few examples of applications in fundamental condensed matter physics, materials science and technology

  16. Pulsed spallation neutron sources

    International Nuclear Information System (INIS)

    Carpenter, J.M.

    1996-01-01

    This paper reviews the early history of pulsed spallation neutron source development ar Argonne and provides an overview of existing sources world wide. A number of proposals for machines more powerful than currently exist are under development, which are briefly described. The author reviews the status of the Intense Pulsed Neutron Source, its instrumentation, and its user program, and provide a few examples of applications in fundamental condensed matter physics, materials science and technology

  17. Reference Sources in Chemistry

    OpenAIRE

    Sthapit, Dilip Man

    1995-01-01

    Information plays an important role in the development of every field. Therefore a brief knowledge regarding information sources is necessary to function in any field. There are many information sources about scientific and technical subjects. In this context there are many reference sources in Chemistry too. Chemistry is one important part of the science which deals with the study of the composition of substances and the chemical changes that they undergo. The purpose of this report is...

  18. Open-Source Colorimeter

    OpenAIRE

    Anzalone, Gerald C.; Glover, Alexandra G.; Pearce, Joshua M.

    2013-01-01

    The high cost of what have historically been sophisticated research-related sensors and tools has limited their adoption to a relatively small group of well-funded researchers. This paper provides a methodology for applying an open-source approach to design and development of a colorimeter. A 3-D printable, open-source colorimeter utilizing only open-source hardware and software solutions and readily available discrete components is discussed and its performance compared to a commercial porta...

  19. Source and replica calculations

    International Nuclear Information System (INIS)

    Whalen, P.P.

    1994-01-01

    The starting point of the Hiroshima-Nagasaki Dose Reevaluation Program is the energy and directional distributions of the prompt neutron and gamma-ray radiation emitted from the exploding bombs. A brief introduction to the neutron source calculations is presented. The development of our current understanding of the source problem is outlined. It is recommended that adjoint calculations be used to modify source spectra to resolve the neutron discrepancy problem

  20. Properties of neutron sources

    International Nuclear Information System (INIS)

    1987-03-01

    The Conference presentations were divided into sessions devoted to the following topics: white neutron sources, primarily pulsed (6 papers); fast neutron fields (5 papers); Californium-252 prompt fission neutron spectra (14 papers); monoenergetic sources and filtered beams (11 papers); 14 MeV neutron sources (10 papers); selected special application (one paper); and a general interest session (4 papers). Individual abstracts were prepared separately for the papers

  1. 3Dmol.js: molecular visualization with WebGL.

    Science.gov (United States)

    Rego, Nicholas; Koes, David

    2015-04-15

    3Dmol.js is a modern, object-oriented JavaScript library that uses the latest web technologies to provide interactive, hardware-accelerated three-dimensional representations of molecular data without the need to install browser plugins or Java. 3Dmol.js provides a full featured API for developers as well as a straightforward declarative interface that lets users easily share and embed molecular data in websites. 3Dmol.js is distributed under the permissive BSD open source license. Source code and documentation can be found at http://3Dmol.csb.pitt.edu dkoes@pitt.edu. © The Author 2014. Published by Oxford University Press.

  2. Optically pumped semiconductor lasers for atomic and molecular physics

    Science.gov (United States)

    Burd, S.; Leibfried, D.; Wilson, A. C.; Wineland, D. J.

    2015-03-01

    Experiments in atomic, molecular and optical (AMO) physics rely on lasers at many different wavelengths and with varying requirements on spectral linewidth, power and intensity stability. Optically pumped semiconductor lasers (OPSLs), when combined with nonlinear frequency conversion, can potentially replace many of the laser systems currently in use. We are developing a source for laser cooling and spectroscopy of Mg+ ions at 280 nm, based on a frequency quadrupled OPSL with the gain chip fabricated at the ORC at Tampere Univ. of Technology, Finland. This OPSL system could serve as a prototype for many other sources used in atomic and molecular physics.

  3. Emission sources and quantities

    International Nuclear Information System (INIS)

    Heinen, B.

    1991-01-01

    The paper examines emission sources and quantities for SO 2 and NO x . Natural SO 2 is released from volcanic sources and to a much lower extent from marsh gases. In nature NO x is mainly produced in the course of the chemical and bacterial denitrification processes going on in the soil. Manmade pollutants are produced in combustion processes. The paper concentrates on manmade pollution. Aspects discussed include: mechanism of pollution development; manmade emission sources (e.g. industry, traffic, power plants and domestic sources); and emission quantities and forecasts. 11 refs., 2 figs., 5 tabs

  4. Advanced Photon Source (APS)

    Data.gov (United States)

    Federal Laboratory Consortium — The Advanced Photon Source (APS) at the U.S. Department of Energy's Argonne National Laboratoryprovides this nation's (in fact, this hemisphere's) brightest storage...

  5. Source SDK development essentials

    CERN Document Server

    Bernier, Brett

    2014-01-01

    The Source Authoring Tools are the pieces of software used to create custom content for games made with Valve's Source engine. Creating mods and maps for your games without any programming knowledge can be time consuming. These tools allow you to create your own maps and levels without the need for any coding knowledge. All the tools that you need to start creating your own levels are built-in and ready to go! This book will teach you how to use the Authoring Tools provided with Source games and will guide you in creating your first maps and mods (modifications) using Source. You will learn ho

  6. Source Reference File

    Data.gov (United States)

    Social Security Administration — This file contains a national set of names and contact information for doctors, hospitals, clinics, and other facilities (known collectively as sources) from which...

  7. Molecular theory of capillarity

    CERN Document Server

    Rowlinson, J S

    2002-01-01

    History of thought on molecular origins of surface phenomena offers a critical and detailed examination and assessment of modern theories, focusing on statistical mechanics and application of results in mean-field approximation to model systems. Emphasis on liquid-gas surface, with a focus on liquid-liquid surfaces in the final chapters. 1989 edition.

  8. Reviews: The Molecular Animator.

    Science.gov (United States)

    Journal of Chemical Education, 1987

    1987-01-01

    Provided is a review of a chemical software package. The package makes possible an instructional technique that is not effective by any other means, namely the ability to view molecular shapes in three dimensions. The program can be used with either IBM or Apple hardware. (RH)

  9. [Towards a molecular psychiatry].

    Science.gov (United States)

    de la Fuente, J R

    1988-06-01

    Recent research data from psychopharmacology, brain imaging and molecular genetics support the notion of a new psychiatric frontier: that of molecular psychiatry. Identification of different subtypes of neurotransmitter receptors and their changes in density and sensitivity in response to endogenous ligands and/or psychotropic drugs may account for the clinical expression of various behavioral phenomena, including some psychiatric disorders. Brain imaging, in particular positron-emission tomographic evaluations, are likely to change psychiatric nosology. New diagnostic elements derived from these scanners will allow to associate psychotic states to neuroreceptor changes. Molecular genetics has shown that bipolar affective disorder can be caused by a single gene. A strong linkage seems to exist between a gene locus on chromosome 11 and bipolar illness. An amyloid gene located on chromosome 21 has also been shown to be strongly related to familial Alzheimer's disease. While genetic heterogeneity limits the screening value of these findings, the powerful techniques of molecular biology have entered the field of psychiatry. Ethical issues regarding DNA immortality, gene cloning and gene therapy will strengthen this relationship.

  10. Molecular studies of achondroplasia

    Directory of Open Access Journals (Sweden)

    Nahar Risha

    2009-01-01

    Full Text Available Background: Achondroplasia (ACH is the most frequent form of short-limbed dwarfi sm, caused by mutations in the FGFR3 gene. It follows an autosomal dominant inheritance, though most cases are sporadic. The molecular techniques are the only available methods to confi rm the diagnosis of a skeletal dysplasia. Clinical and radiological features are only suggestive and not confi rmatory. The present study was conducted to fi nd out how often the clinical diagnosis of achondroplasia is verifi ed on molecular studies. Materials and Methods: From 1998 through 2007, we carried out molecular analysis for the two common mutations in the FGFR3 gene in 130 cases clinically suspected to have ACH. Results: A diagnostic mutation was identifi ed in 53 (40.8% cases. The common mutation (1138G>A was present in 50 (94.7% of the positive cases, while the rare 1138 G>C substitution was found in three (5.3%. Conclusion: This study shows that confi rmation of clinical diagnosis of ACH by molecular genetic testing is essential to distinguish it from other skeletal dysplasias, to plan therapeutic options, and to offer genetic counseling. Management (medical and surgical in patients confi rmed to have ACH, is briefl y discussed.

  11. Molecular diagnosis and immunotherapy.

    Science.gov (United States)

    Sastre, Joaquín; Sastre-Ibañez, Marina

    2016-12-01

    To describe recent insights into how molecular diagnosis can improve indication and selection of suitable allergens for specific immunotherapy and increase the safety of this therapy. As specific allergen immunotherapy targets specific allergens, identification of the disease-eliciting allergen is a prerequisite for accurate prescription of treatment. In areas of complex sensitization to aeroallergens or in cases of hymenoptera venom allergy, the use of molecular diagnosis has demonstrated that it may lead to a change in indication and selection of allergens for immunotherapy in a large proportion of patients when compared with diagnosis based on skin prick testing and/or specific IgE determination with commercial extracts. These changes in immunotherapy prescription aided by molecular diagnosis have been demonstrated to be cost-effective in some scenarios. Certain patterns of sensitization to grass or olive pollen and bee allergens may identify patients with higher risk of adverse reaction during immunotherapy. Molecular diagnosis, when used with other tools and patients' clinical records, can help clinicians better to select the most appropriate patients and allergens for specific immunotherapy and, in some cases, predict the risk of adverse reactions. The pattern of sensitization to allergens could potentially predict the efficacy of allergen immunotherapy provided that these immunotherapy products contain a sufficient amount of these allergens. Nevertheless, multiplex assay remains a third-level approach, not to be used as screening method in current practice.

  12. Isotopes in molecular biology

    International Nuclear Information System (INIS)

    Goldfarb, P.S.G.

    1988-01-01

    The use of radioisotopes in molecular biology, with particular reference to the structure and functions of DNA, RNA and the cellular synthesis of proteins, is discussed. The use of labelled DNA and RNA in diagnostic techniques is presented. (U.K.)

  13. Biophysics of molecular gastronomy.

    Science.gov (United States)

    Brenner, Michael P; Sörensen, Pia M

    2015-03-26

    Chefs and scientists exploring biophysical processes have given rise to molecular gastronomy. In this Commentary, we describe how a scientific understanding of recipes and techniques facilitates the development of new textures and expands the flavor palette. The new dishes that result engage our senses in unexpected ways. PAPERCLIP. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Molecular gastronomy in Spain

    DEFF Research Database (Denmark)

    García-Segovia, P.; Garrido, M. D.; Vercet, A.

    2014-01-01

    Beyond the overwhelming international success of Ferrán Adria, Spain has been one of the countries with a more active implication in molecular gastronomy as a scientific discipline but also in the use of ingredients, technologies, and equipment from the scientific and technological universe...... with scientists for facing the future of Spanish gastronomy....

  15. Molecular Mechanisms of Preeclampsia

    Directory of Open Access Journals (Sweden)

    N. Vitoratos

    2012-01-01

    Full Text Available Preeclampsia is one of the leading causes of maternal morbidity/mortality. The pathogenesis of preeclampsia is still under investigation. The aim of this paper is to present the molecular mechanisms implicating in the pathway leading to preeclampsia.

  16. Molecular MR Imaging Probes

    OpenAIRE

    MAHMOOD, UMAR; JOSEPHSON, LEE

    2005-01-01

    Magnetic resonance imaging (MRI) has been successfully applied to many of the applications of molecular imaging. This review discusses by example some of the advances in areas such as multimodality MR-optical agents, receptor imaging, apoptosis imaging, angiogenesis imaging, noninvasive cell tracking, and imaging of MR marker genes.

  17. Molecular dynamics for fermions

    International Nuclear Information System (INIS)

    Feldmeier, H.; Schnack, J.

    2000-02-01

    The time-dependent variational principle for many-body trial states is used to discuss the relation between the approaches of different molecular dynamics models to describe indistinguishable fermions. Early attempts to include effects of the Pauli principle by means of nonlocal potentials as well as more recent models which work with antisymmetrized many-body states are reviewed under these premises. (orig.)

  18. Nanopatterning by molecular polygons.

    Science.gov (United States)

    Jester, Stefan-S; Sigmund, Eva; Höger, Sigurd

    2011-07-27

    Molecular polygons with three to six sides and binary mixtures thereof form long-range ordered patterns at the TCB/HOPG interface. This includes also the 2D crystallization of pentagons. The results provide an insight into how the symmetry of molecules is translated into periodic structures.

  19. Molecular radio-oncology

    Energy Technology Data Exchange (ETDEWEB)

    Baumann, Michael; Krause, Mechthild; Cordes, Nils (eds.) [Technische Univ. Dresden (Germany). Faculty of Medicine and University Hospital

    2016-07-01

    This book concisely reviews our current understanding of hypoxia, molecular targeting, DNA repair, cancer stem cells, and tumor pathophysiology, while also discussing novel strategies for putting these findings into practice in daily clinical routine. Radiotherapy is an important part of modern multimodal cancer treatment, and the past several years have witnessed not only substantial improvements in radiation techniques and the use of new beam qualities, but also major strides in our understanding of molecular tumor biology and tumor radiation response. Against this backdrop, the book highlights recent efforts to identify reasonable and clinically applicable biomarkers using broad-spectrum tissue microarrays and high-throughput systems biology approaches like genomics and epigenomics. In particular, it describes in detail how such molecular information is now being exploited for diagnostic imaging and imaging throughout treatment using the example of positron emission tomography. By discussing all these issues in the context of modern radiation oncology, the book provides a broad, up-to-date overview of the molecular aspects of radiation oncology that will hopefully foster its further optimization.

  20. Molecular radio-oncology

    International Nuclear Information System (INIS)

    Baumann, Michael; Krause, Mechthild; Cordes, Nils

    2016-01-01

    This book concisely reviews our current understanding of hypoxia, molecular targeting, DNA repair, cancer stem cells, and tumor pathophysiology, while also discussing novel strategies for putting these findings into practice in daily clinical routine. Radiotherapy is an important part of modern multimodal cancer treatment, and the past several years have witnessed not only substantial improvements in radiation techniques and the use of new beam qualities, but also major strides in our understanding of molecular tumor biology and tumor radiation response. Against this backdrop, the book highlights recent efforts to identify reasonable and clinically applicable biomarkers using broad-spectrum tissue microarrays and high-throughput systems biology approaches like genomics and epigenomics. In particular, it describes in detail how such molecular information is now being exploited for diagnostic imaging and imaging throughout treatment using the example of positron emission tomography. By discussing all these issues in the context of modern radiation oncology, the book provides a broad, up-to-date overview of the molecular aspects of radiation oncology that will hopefully foster its further optimization.